With the current increase in frequency of coral bleaching events, knowledge on the genetic diversity of symbiotic algae in the genus Symbiodinium harboured by reef-building corals is important to understand how coral reefs will respond to global climate change. This study was undertaken as very little is known about the subject in reef-building corals in Tanzania and yielded information on the genetic diversity of Symbiodinium in 66 scleractinian coral species from 19 common genera. The internal transcribed spacer two (ITS-2) region in nuclear ribosomal DNA (rDNA) was used to identify the symbiont types following polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequencing. ITS-2 Symbiodinium types from clades A, C and D, previously reported in corals from other regions, were detected. While ITS-2 sequences from Symbiodinium clade C varied significantly, those from clades D and A did not. Most reef-building corals were found to be poor at forming symbioses with multiple symbiotic algae, indicating low adaptability to environmental change. This study followed ten years after the 1998 coral bleaching event and thus provided information needed for studies on temporal changes in Symbiodinium diversity in Tanzanian corals, especially in relation to large-scale bleaching events.