Didemnid family ascidians commonly harbor obligate cyanobacterial symbionts, Prochloron spp., which have been proposed to biosynthesize cyclic peptides. Here, it is shown that Prochloron spp. do indeed contain genes for nonribosomal peptide biosynthesis, although genes for cyclic peptide biosynthesis have not yet been characterized. A peptide synthetase-containing open reading frame of unknown function was cloned from the Prochloron symbionts of some didemnid ascidians, but not from others. These data indicate that Prochloron spp. have variable secondary metabolic potential.