The Psalms - Psalm 99
The Holy God
by Rev. James Jester
November 2, 2025
SCRIPTURE READING: Isaiah 6:1-3
“In the year that king Uzziah died I saw also the Lord sitting upon a throne, high and lifted up, and his train filled the temple. 2 Above it stood the seraphims: each one had six wings; with twain he covered his face, and with twain he covered his feet, and with twain he did fly. 3 And one cried unto another, and said, Holy, holy, holy, is the LORD of hosts: the whole earth is full of his glory.”
INTRODUCTION
Psalm 99 is a triple proclamation of God’s holiness, as Isaiah would do at a later date, and as we read: “Holy, holy, holy, is the LORD of hosts”(Isa. 6:3). The two divisions of the psalm (v. 1-5, 6-9) both end in the refrain exhorting the worshippers to exalt the God who is holy (v. 5, 9). This psalm is a call to praise God because of the glories (and blessings) of His Kingdom among men (Adamkind). It is a song of praise describing Christ’s reign.
GOD IS IN HIS SANCTUARY (v. 1):
“The LORD reigns; Let the people tremble! He dwells between the cherubim; Let the earth be moved!” (Ps. 99:1, NKJV)
The LORD reigns: For the fourth time, a psalm begins with this phrase (see also Ps. 93:1; 96:10; 97:1; 99:1). Psalm 99 speaks of God’s presence — He has accepted His royal rule (Rev. 19:6), and then sits “upon the throne of his glory” (Matt. 25:31). At this point, Jesus the Christ is not only seated on His Father’s throne (Rev. 3:21), but He is now also seated on His own throne, along with the remnant over-comers. It is not that He is simply present there; He is a reigning king.
Let the people tremble: The Septuagint and the Latin Vulgate render this, “Let the people rage” or, be angry; as if the idea were that God reigned, even though the people were opposed to Him. The true meaning of the word used here, however, is “tremble,” properly meaning, to be moved, or disturbed. It may also mean to be moved with anger (Pro. 29:9); or with grief (2 Sam. 18:33), or with fear (Ps. 4:4), or with joy (Jer. 33:9). Hence, it means to be agitated or moved with fear or reverence. So, in the presence of a sovereign God, it is appropriate to “tremble.” The quaking of the earth in this verse, “let the earth be moved,” is nature’s counterpart to the trembling of the people.
He dwells between the cherubim: This phrase appears only here in the Old Testament. It refers to the cherubim of the mercy seat where God met with his people. “When Moses entered the Tent of Meeting to speak with the LORD, he heard a voice speaking to him above the Mercy Seat over the Ark of the Testimony. He spoke to him from between the two cherubim.” (Num. 7:89, ISV)
The Hebrew word translated “dwell” is literally “to sit,” picturing God as a King sitting on his throne. It is difficult to say whether the psalmist had in mind the heavenly sanctuary of God or the earthly representation of it (the tabernacle or temple); both are true and either one fits.
“When Moses went into the tabernacle of meeting to speak with Him, he heard the voice of One speaking to him…” (Num. 7:89a, NKJV). I believe that Moses heard the Voice of Jesus conversing with him. Great is the condescension of the Lord in thus speaking with Moses, and through Moses to the people. Let us notice here: 1) The sacred place in which He speaks; it was in the holy of holies in “the tabernacle of meeting.” It was in this place that he had promised to meet with His servant. 2) He is represented as dwelling in this place, and as enthroned between the cherubim. It was the place of His special self-manifestation.
The mercy-seat was the massive golden cover of the ark of the covenant, on which the glory of God appeared between the cherubim. It was here, on and around the mercy-seat, where the blood of the propitiatory sacrifice was sprinkled on the day of atonement (Lev. 16:15).
The mercy-seat is a figure, or a type, of the Lord Jesus Christ. He is the true Mercy-seat, “Whom God hath set forth to be a propitiation through faith in his blood, to declare his righteousness for the remission of sins that are past, through the forbearance of God” (Rom. 3:25). By the shedding of His blood, the great atonement for the sins of the covenant people was made.
GOD IS PRESENT IN ZION (v. 2-3):
“The LORD is great in Zion, And He is high above all the people. Let them praise Your great and awesome name— He is holy.” (Ps. 99:2-3, NKJV)
The LORD is great in Zion: The LORD and Zion is not a matter of comparison, to show which is the greatest. God “is great” in Himself. There is simply no one to compare to Him. He is great, and Israel knows that God is great; “For the LORD your God is God of gods, and Lord of lords, a great God, a mighty, and a terrible, which regardeth not persons, nor taketh reward” (Deut. 10:17). Now all the nations must acknowledge that fact.
He is high above the people: The custom of ancient times in the East is described in the Pulpit Commentary: “Eastern thrones were high erections, so that the king, seated in his place, might be exalted ‘high above the people.’ The seat was reached by a series of steps; the bottom step was known as the ‘king’s footstool,’ and the suppliant for the king’s mercy, or the man who brought presents as signs of loyalty, showed his humility and reverence by venturing no further than the footstool. Solomon had made a throne of ivory, overlaid with gold, which had six steps, with six lions on each side. Salutations in the East were very elaborate, and approaches to a superior, especially when a request had to be made, involved bending right to the ground.” (P. C.)
God is present in heaven and in all the earth, but He has special regard for “Zion,” the city of Jerusalem. In that city set in the hills, He is “high above the people.” This is also true of the New Jerusalem. But “Zion” ultimately means the entire company of the faithful:
“But ye are come unto mount Sion, and unto the city of the living God, the heavenly Jerusalem, and to an innumerable company of angels, 23 To the general assembly and church of the firstborn, which are written in heaven, and to God the Judge of all, and to the spirits of just men made perfect, 24 And to Jesus the mediator of the new covenant, and to the blood of sprinkling, that speaketh better things than that of Abel.” (Heb. 12:22-24)
Let them praise Your great and awesome name: God rightfully receives praise because of His greatness and character.
He is holy: Holiness, at its root, has the idea of separateness. It describes someone, or something, which is set apart from other people or things. An object can be holy if it is set apart for sacred service. A person is holy if he is set apart for God’s purpose and will. Holiness also carries with it the moral sense, as between the pure and the polluted. This includes the genetic sense as well, or God would not have brought judgment in the days of Noah.
God Himself is set apart in many ways. He is set apart from creation, in that He is not a creature. He also exists outside of creation. If all creation were to dissolve, the Lord God would remain. He is set apart from humanity and mortality, in that His nature is Divine, not human. Holiness is the essence of His entire Being.
THE STRONG RIGHTEOUSNESS OF GOD (v. 4):
“The King’s strength also loves justice; You have established equity; You have executed justice and righteousness in Jacob.” (Ps. 99:4)
The King’s strength also loves justice: God’s great strength could, in theory, be used for evil. Yet the King “loves justice” and has “established equity” in His decisions. God does not abuse his power by tyranny, but connects it with justice and fairness.
You have executed justice: With God, justice and equity (fairness) are not mere slogans or promises. He has “executed justice and righteousness” among His people, Jacob/Israel. This is a figure of that great salvation provided for us in Jesus the Christ. God’s supremacy is in both the church and the state.
THE RESPONSE TO HIS HOLY STRENGTH (v. 5):
“Exalt the LORD our God, And worship at His footstool— He is holy.” (Ps. 99:5, NKJV)
Exalt the LORD our God: Understanding the power, holiness, and goodness of God should lead us to exalt Him and humbly worship Him.
Worship at His footstool: Most commentators regard this as the ark of the covenant, connected to their understanding of “between the cherubim” in verse 1. The ark of the covenant is called His footstool in 1 Chronicles 28:2, but so are Jerusalem (Lam. 2:1) and the earth as a whole (Isa. 66:1, Matt. 5:35). The covenant people (“in Jacob,” v. 4) are to have a distinctive role in praising and worshipping God at “His footstool.”
He is holy: The statement from verse three is repeated for emphasis. God “is holy” in all He is and does. The Bible calls God holy more than anything else, more than sovereign, more than just, more than loving, etc. In fact “holy” is the only epithet of God that is repeated three times for emphasis: “Holy, holy, holy” (Isa. 6:3; Rev. 4:8). Holiness is the harmony of all the various virtues.
GOD IS REVEALED TO HIS PRIESTS (v. 6-7):
“Moses and Aaron were among His priests, And Samuel was among those who called upon His name; They called upon the LORD, and He answered them. He spoke to them in the cloudy pillar; They kept His testimonies and the ordinance He gave them.” (Ps. 99:6-7, NKJV)
Moses and Aaron were among His priests: Priests are servants or intercessors. The psalmist listed three notable priests in the history of Israel: Moses, Aaron, and Samuel. These were the ones who prayed (“called upon His name”) and God revealed Himself (“He answered them”). They interceded on behalf of Israel.
Of these, Aaron only was a priest in the usual meaning of the term. But Moses discharged the priestly duties (Ex. 24:1-18) before Aaron entered upon his office, and he consecrated Aaron and his sons (Lev. 8:1-36). Likewise, Moses constructed and conducted the first celebration of worship in the Tabernacle (Ex. 40:18-33):
“Moses erected the tabernacle; he laid its bases, and set up its frames, and put in its poles, and raised up its pillars; 19 and he spread the tent over the tabernacle, and put the covering of the tent over it, as the LORD had commanded Moses. 20 And he took the testimony and put it into the ark, and put the poles on the ark, and set the mercy seat above on the ark; 21 and he brought the ark into the tabernacle, and set up the veil of the screen, and screened the ark of the testimony; as the LORD had commanded Moses. 22 And he put the table in the tent of meeting, on the north side of the tabernacle, outside the veil, 23 and set the bread in order on it before the LORD; as the LORD had commanded Moses. 24 And he put the lampstand in the tent of meeting, opposite the table on the south side of the tabernacle, 25 and set up the lamps before the LORD; as the LORD had commanded Moses. 26 And he put the golden altar in the tent of meeting before the veil, 27 and burnt fragrant incense upon it; as the LORD had commanded Moses. 28 And he put in place the screen for the door of the tabernacle. 29 And he set the altar of burnt offering at the door of the tabernacle of the tent of meeting, and offered upon it the burnt offering and the cereal offering; as the LORD had commanded Moses. 30 And he set the laver between the tent of meeting and the altar, and put water in it for washing, 31 with which Moses and Aaron and his sons washed their hands and their feet; 32 when they went into the tent of meeting, and when they approached the altar, they washed; as the LORD commanded Moses. 33 And he erected the court round the tabernacle and the altar, and set up the screen of the gate of the court. So Moses finished the work.” (Ex. 40:18-33, RSV)
Samuel also exercised priestly functions (1 Sam. 7:9; 9:12-13). The main feature of the priestly office which is here brought into view is intercession. Examples of this calling upon God by Moses are recorded in Exodus 17:11-12; 32:30-32; Psalm 106:23; and by Samuel in 1 Samuel 7:8-9; 12:16-23. An example of the efficacy of Aaron’s intercession is recorded in Numbers 16:47-48.
Among those who called upon His name: Intercessions and pleadings such as theirs — so bold, yet so reverent; so confident, yet so humble — greatly honor the Lord. Their living faith in Him and their sincere trust in His mercy were pleasing to Him. “He that cometh to God must believe that He is, and that He is a rewarder of them that diligently seek Him.” (Heb. 11:6)
He spoke to them in the cloudy pillar: The pillar of cloud was the physical representation of God’s presence with Israel in the wilderness. God spoke to Moses from that “cloudy pillar” (Ex. 33:9).
They kept His testimonies: The psalmist noted the general obedience of Moses, Aaron, and Samuel. Since they listened to Him and obeyed; therefore, He listened to them and answered their prayer. This is always the pattern for Christians.
GOD IS REVEALED IN FORGIVENESS AND HOLINESS (v. 8-9):
“You answered them, O LORD our God; You were to them God-Who-Forgives, Though You took vengeance on their deeds. Exalt the LORD our God, And worship at His holy hill; For the LORD our God is holy.” (Ps. 99:8-9, NKJV)
You were to them God-Who-Forgives: God answered these men (and others) who sought Him. He revealed Himself to them as the “God-Who-Forgives.” Even these men of whom it was said, “they kept His testimonies” (v. 7) need this revealing of forgiveness. Forgiveness is stressed over and over again in Scripture. In the words of our Lord Jesus, “For if ye forgive men their trespasses, your heavenly Father will also forgive you” (Matt. 6:14).
Though You took vengeance on their deeds: It isn’t clear if the ones referred to here are the priests mentioned in verse 6 (Moses, Aaron, and Samuel) or if it is referring to the people they prayed for (Israel as a whole). Most Bible students regard “their deeds” as referring to Israel’s deeds, but it also is true that Moses, Aaron, and Samuel were disciplined by God in some way. The mention of God’s forgiveness and vengeance refers primarily to the repeated failures within Israel’s history.
“Vengeance” does not mean revenge. The punishment of a criminal by the state is not an act of revenge, but the due maintenance of righteous law. This maintenance is necessary for the preservation of society, and sometimes even for the reformation of the criminal himself.
While God forgives, it does not cancel all the consequences of sin. This is a part of vengeance. From the Preacher’s Homiletical:
“Whatever painful consequences of past sin may still linger about our lives, or haunt our hearts, we may be sure of two things about them all—that they come from forgiving mercy, that they come for our profit. It is no harsh, nor even only a righteous Judge who deals with us. We are chastened by a Father’s hand. ‘When we are judged, we are chastened of the Lord, that we should not be condemned’ (1 Cor. 11:32). The stroke of condemnation will never fall upon our pardoned hearts.” (P. H.)
God spared them, but showed his displeasure toward their deeds. He chastised, but did not consume Israel, because He is their Father.
Exalt the LORD our God: Once more the psalmist is compelled to exalt God. The great subject of the psalmist’s praise is the holiness of God. It is a holy God that calls upon all of Adamkind to worship. It is a holy worship, and such was the worship of the saints of old. Then likewise, God revealed His holiness both in forgiving and in taking vengeance.
For the LORD our God is holy: For the emphatic third time, God’s holiness is proclaimed. Later, in heavenly visions, the Prophet Isaiah (Isa. 6:3) and the Apostle John (Rev. 4:8) would hear this triplet declaration of holiness combined into a single sentence.
CONCLUSION
“Holy, holy, holy, is the LORD of hosts: the whole earth is full of his glory.” (Isa. 6:3)
It seems that all of God’s people have a “vision” of the Lord at one time or another in their life. For Isaiah, it was after king Uzziah had died. This was the beginning of the prophet’s call to his mission. The prophet also had a vision of himself (v. 5), a vision of cleansing (v. 6-7), a vision of the need (v. 8), a vision of judgment (9-12), and a vision of hope (v. 13). Likely, every Christian goes through such a spiritual process with the Lord. We should ask: “What event in your life turned your heart toward the Holy God?”
How holy are all the doings of God our Father and the Lord Jesus Christ! All the attributes and acts of God are gloriously symmetrical, they harmonize. Because we are reconciled to God through Jesus, we may approach His throne. Jesus is the King, the Mercy Seat is the throne, and the scepter which He sways is holy, like Himself. As we exalt Him, let us draw near in humility and adoration. There’s only one kingdom, and there’s only one Holy God. All other gods are counterfeit.
