An epithalamion is a poem celebrating marriage, so the main theme of Spenser's Epithalamion is to celebrate and invoke a blessing on a marriage. The speaker asks the muses for a blessing, awakes his bride, invites nymphs and goddesses to his wedding, as well as children, and asks for good weather. All of this imbues the marriage with a sacred aura that unites the pagan and the Christian as one, a typical Renaissance move that is a second theme: the poem suggests that both Classical literature and Christianity point to the same divine source, though Christianity understands it more fully.

Christian elements are more pronounced when the speaker describes his wife-to-be as angel:

Clad all in white, that seems a virgin best. So well it her beseemes that ye would weene, Some angell she had beene.

The speaker's praises of his beloved's beauty, though more chaste, are reminiscent too of the biblical Song of Solomon. And as the bride and groom enter the temple where the marriage takes place, the imagery becomes increasingly Christian, with organs, a choir, a priest, and angels singing alleluia.

As part of celebrating marriage, the poem also emphasizes the importance of the bride's adoration of the husband and the importance of children as an outcome of marriage. The speaker wishes for “fruitfull progeny” or many children from the union, as well as for the birth of "blessed Saints," showing that despite all the rich Classical imagery, this is a Christian union.

All in all, the chief message or theme of this poem is that marriage is a deeply and richly sacred union.