The aeolid nudibranch Pteraeolidia ianthina hosts symbiotic dinoflagellates in the same way as many reef-building corals. This widespread Indo-Pacific sea slug ranges from tropical to temperate waters, and offered a unique opportunity to examine a symbiosis that occurs over a large latitudinal gradient. We used partial 28S and 18S nuclear ribosomal (nr) DNA to examine the genetic diversity of the Symbiodinium dinoflagellates contained within Pteraeolidia. We detected Symbiodinium from genetic clades A, B, C and D. Pteraeolidia ianthina from tropical regions (Singapore, Sulawesi) host Symbiodinium clade C or D or both, those from the subtropical eastern Australian coast (Heron Island, Mon Repo, Moreton Bay, Tweed Heads) host clade C Symbiodinium but those from the temperate south eastern Australian coastline (Port Stephens, Bare Island), host clade A or B or both. The Symbiodinium populations within one individual nudibranch could be homogeneous or heterogeneous at inter- or intra-clade levels (or both). The results suggested that the Pteraeolidia-Symbiodinium symbiosis is flexible and favours symbiont phylotypes best adapted for that environment. This flexibility probably reflects the function of the symbiont clade in relation to the changing environments experienced along the latitudinal range, and facilitates the large geographic range of Pteraeolidia ianthina.