The identity and diversity of algal symbionts (Symbiodinium spp.) in reef corals is thought to influence to the resilience of reef ecosystems to climate change, and varies depending on coral species, environmental conditions, and biogeography. We examined these factors by surveying corals along a latitudinal gradient in Western Australia on reefs connected north to south by the warm-water Leeuwin Current. We used the internal transcribed spacer-2 (ITS-2) region of ribosomal DNA to characterize Symbiodinium communities in 19 species of reef coral (in 16 genera) from tropical Dampier (20.5°S) to temperate Dunsborough (33.5°S). We documented a high number of novel ITS-2 types in Symbiodinium clades B (1 type) and C (14 types) as well as 7 previously reported ITS-2 types in clades B, C, and D. In addition, we compared symbiont distributions with Giovanni's OBIG MODIS-Aqua satellite temperature data set and found that the putatively thermotolerant Symbiodinium ITS-2 type D1a was more frequently detected in 'chronically warm' tropical sites than at 'chronically cool' temperate sites, while clade B symbiont types showed the reverse pattern, being found in certain corals at the southernmost sites. Symbiodinium type D1a was generally most abundant at Dampier, where bleaching had occurred 1 mo prior to sampling, although some variation by host taxa was observed. The diverse and novel Symbiodinium communities documented here may be a result of (1) the variable environmental histories of the study sites, (2) the apparent genetic divergence within this genus resulting from the relative isolation of Western Australian reefs, and/or (3) the frequent transport of symbionts (in hospite or free-living) from Indo-Malay reefs to Western Australia via the Leeuwin Current. These results indicate that understudied reefs in remote and isolated areas may contain Symbiodinium diversity that has not been reported previously.