The internal transcribed spacer (ITS) regions from 47 Symbiodinium (Freudenthal) isolates cultured from 34 different host species and two populations sampled from nature were sequenced and compared. Of these, 17 distinct ITS types were identified. The described species Symbiodinium goreaui, S. kawagutii, S. pilosum (Trench and Blank), S. microadriaticum (Freudenthal), and S. (=Gymnodinium) linucheae (Trench and Thinh) had ITS sequences distinct from each other. Four of these species share identical ITS sequences with uncharacterized isolates. Sequence differences among other isolates indicate that at least seven other cultured types await formal species descriptions, whereas numerous others most likely exist in nature. The Symbiodinium phylogeny is positively correlated with cell size, mycosporine-like amino acid production (UV protection), and host infectivity, whereas the production of water-soluble peridinin–chl a–protein homodimer and monomer apoproteins and isoenzyme similarity do not correlate. There is evidence, based on the lack of phylogenetic congruency with allelic variability, that sexual recombination occurs at some frequency among Symbiodinium populations. Symbiodinium isolates from the Caribbean possess identical ITS sequences to isolates originating from the Red Sea or the western Pacific. These findings indicate that some Symbiodinium species may have global biogeographic distributions.