The apse mosaic dates from the 6th century and depicts two scenes that blend into each other. At the top is an interestingly symbolic depiction of the Transfiguration (Mt 17:1-9). Christ is represented by a golden cross on a starry blue background, while the three apostles who were present at the Transfiguration - Peter, James and John - are represented by lambs. Flanking the cross against a backdrop of golden skies and sunset-tinged clouds are figurative depictions of Moses and Elijah, labeled with their names. The large cross is decorated with mosaic gems and a bust of Christ in the center. It has a Latin inscription at its base reading SALVS MVNDI, "Salvation of the World" and a Greek inscription at the top: IXΘYC. This means "fish" in Greek and is also an anagram of the names of Christ: Jesus Christ Son of God Savior."
Below this scene is the namesake of the basilica, labeled with the inscription SANCTVS APOLENARIS. He is shown in prayer, interceding on behalf of his flock who are represented below by lambs. This is the first known example of choosing a subject other than Christ in Majesty for the apse decoration. Around the saint is a soft green backdrop populated with rocks, birds, and plants. Among the greenery are pine trees, which can still be seen growing outside the church.