The LORD reigns is mentioned for the fourth time (Psalms 93:1; 96:10; 97:1; 99:1). He has accepted His royal rule (Revelation 19:6) and sits on His glorious throne (Mat_25:31). Now Christ is not only seated on His Father's throne (Revelation 3:21), He is now also seated on His own throne along with the overcomers, the remnant. He is truthfully "the King of kings and Lord of lords" (1Timothy 6:15).
God's holiness, too, is emphasised in the refrain of Psalm 99:3, 99:5, 99:9. The Psalm begins with a call to worship God with the awe and reverence which are due to Him (v. 1~3). His righteous rule in Israel, is a reason for repeating the summons (v. 4~5). The history of His dealings with His people from the days of Moses and Aaron to the time of Samuel is summed up (v. 6~8). Verse 9 is almost a repetition of verse 5, and implies that the Temple has been restored.