Two didemnid ascidians associating with cyanobacterial symbionts (Prochloron spp.) were firstly recorded from Caribbean Panama: Lissoclinum verrilli, which facultatively harboured Prochloron cells on the colony surface, and Diplosoma simile, which obligately harboured algal cells in the peribranchial and common cloacal cavities within the colonies. While L. verrilli sensu stricto has been exclusively recorded from the Bermudas and Caribbean islands, D. simile is widely distributed in tropical Indo-Pacific regions including oceanic islands such as Hawaii. Partial COI sequences of D. simile from the Caribbean were identical to those from the West Pacific, suggesting a high larval-dispersal ability and broad range of environmental tolerance. Molecular phylogenetics of the symbionts, based on 16S rRNA gene sequences, revealed that both ascidian species were associated with Prochloron, while a Synechocystis sp. sequence was also obtained for L. verrilli. In addition, L. verrilli and D. simile harboured different phylotypes within the Prochloron lineage that included symbionts from various hosts and various Pacific sites. Our results indicate that multiple phylotypes of Prochloron exist in Caribbean Panama and that considering the abundance and the number of host species in the Pacific, Prochloron and D. simile may have come from tropical Indo-West Pacific.