The island continent of Madagascar spans nearly 13.5o of latitude in the SW Indian Ocean. Its coastline includes a number of well developed coral reefs, ranging from tropical Nosy Bé (NW Madagascar, 12oS) and Vohemar (Volhmarina, NE Madagascar, 13oS) to subtropical Tuléar (Toliara , SW Madagascar, 23.5oS), as well as temperate coral communities at Fort Dauphin (Tolagnaro, SE Madagascar, 25oS). Given the range of environmental conditions experienced by reef corals at these different sites, Madagascar represents an ideal location to study the distribution of algal symbionts (Symbiodinium spp.) in these coral hosts. To investigate the effect of latitudinal gradients in temperature on Symbiodinium distributions, 220 samples from 27 coral genera in 12 families were collected from these 4 sites in September 2001. To test the stability of these distributions over time, a further 337 samples were collected from the Nosy Bé and Tuléar regions in March 2007 and November 2009. Symbiodinium communities were screened using Denaturing Gradient Gel Electrophoresis (DGGE) to analyze the internal transcribed spacer-2 (ITS-2) region of Symbiodinium ribosomal DNA, with individual symbiont taxa identified by sequencing individual DGGE bands. Significant differences were found in the Symbiodinium cladal composition of reef corals at different sites, with corals at northern sites containing a higher relative frequency of Symbiodinium in clade D (occurring as mixed clade C+D communities) than southern sampling sites. Nominal logistic analysis of the distribution of symbionts found a significant effect of coral taxa and site, but not of sea surface temperature metrics (environmental data obtained from NOAA’s Coral Reef Watch satellite-derived data) in determining the distribution of different symbionts. Rarefaction analysis indicated there were no differences in Symbiodinium richness (at either the clade or the subtype level) between different sites, or between different sampling intervals. Differences existed in the subcladal composition of dominant ITS-2 types found in congeners at different latitudes, with corals in the genus Acropora being dominated by Symbiodinium C3 (specifically subtype C3z) in northern sites, and C1 in southern sites. Symbiont communities changed between 2001 and 2007/2009, with increases in mixed Symbiodinium C+D assemblages occurring at southern sites that had experienced temperature stress during the intervening period. Decreases in mixed Symbiodinium communities occurred at northern sites, which were not as severely affected by thermal stress. It is suggested that the latitudinal gradients in Symbiodinium found in Madagascar, and the environmental controls on community structure described here, provide important insight into how coral species in this understudied area can adapt or acclimatize to changing environmental conditions through shifts in the composition of their symbiont communities. This will help improve our understanding of how projected climate change in the SW Indian Ocean will affect survival trajectories for coral reefs in the region.