ABSTRACT: The formation and persistence of modern coral reefs depends largely on organisms that host dinoflagellate algal symbionts of the genus Symbiodinium. There are important ecological and physiological differences among Symbiodinium types, and many host species are able to associate with multiple types, which may facilitate adaptation to local environmental change. Using denaturing gradient gel electrophoresis (DGGE) and sequencing of internal transcribed spacer-2 (ITS2) ribosomal DNA, we identified 11 Symbiodinium types belonging to clades A, C, and D in 250 host animals from 3 Tridacna species in eastern Indonesia. Individuals with multiple symbiont types were common: 42% of all clams had symbionts from multiple clades and 15% of all clams had multiple types from a single clade. T. crocea associated more often with clade C symbionts and less frequently with clade D symbionts. T. squamosa associated more frequently with clade D and less often with clade C symbionts. T. maxima did not preferentially associate with a particular Symbiodinium clade, but sample sizes were low. We used both satellite sea surface temperature and in situ recordings to characterize the thermal environment in the study area. Clams with clade C and D symbionts were located in areas with higher mean temperatures, while clams with clade A symbionts were in cooler areas. This is consistent with previous research indicating that clade C and D types may be more heat-tolerant than clade A. These results support the hypothesis that giant clams can associate with different symbiont types based on local environmental conditions.