The external surfaces of marine animals are colonized by a wide variety of epibionts. Here, we study the phototrophic epibiotic community attached to the colonial ascidian Cystodytes dellechiajei collected in the Mediterranean Sea. Epifluorescence microscopy analysis showed abundant filamentous cyanobacteria on the upper and basal parts of the ascidian that displayed autofluorescence, as well as some unicellular cyanobacteria, diatoms, and structures, which could belong to microscopic rhodophyte algae. In addition, high-performance liquid chromatography of the photosynthetic pigments confirmed that the phototrophic epibionts possess chlorophyll (Chl) d, as well as Chl a, b, and c, which enable them to use far-red light for photosynthesis in that peculiar microenvironment. Furthermore, laser scanning confocal microscopy showed the presence of a few small patches of cells on the basal part of the ascidian displaying fluorescence between 700 and 750 nm after excitement with a 635-nm red laser, typically within the range of Chl d. Denaturing gradient gel electrophoresis of the 16S rRNA gene polymerase chain reaction amplified using specific primers for Cyanobacteria detected sequences related with the genera Planktothricoides, Synechococcus, Phormidium, and Myxosarcina, as well as sequences of chloroplasts of diatoms and rhodophyte algae. Remarkably, only the sequences related to the filamentous cyanobacteria Planktothricoides spp. and some chloroplast sequences were found in almost all specimens collected under different macroecological conditions and geographical areas, suggesting thus certain specificity in the epibiotic association. On the other hand, Prochloron spp. and Acaryochloris marina, typically associated to tropical ascidians, were not detected by denaturing gradient gel electrophoresis. However, given the low abundance of cells displaying Chl d in C. dellechiajei and the fact that molecular fingerprinting techniques not always recover low abundance groups, the presence of these cyanobacteria cannot be ruled out. Nevertheless, our data indicate that tropical ascidians and C. dellechiajei differ in their phototrophic communities, although Chl d-containing cells are present in both microenvironments.