The aim of this research was to analyze the phylogenetic relationships of zooxanthellate bivalves belonging to the genera Tridacna, Hippopus, Fragum, and Corculum as well as to the closely related azooxanthellate bivalves belonging to Vasticardium and Fulvia. The small-subunit ribosomal RNA genes (18S rDNAs) from these bivalves were amplified by polymerase chain reaction with universal eukaryotic primers and were then sequenced. The sequence data from each species were analyzed by the neighbor-joining, maximum parsimony, and maximum likelihood methods, and phylogenetic trees were constructed. The results were essentially consistent with the morphological taxonomy of these bivalves. Thus, the zooxanthellate clams branch into two lineages, one composed of the genera Fragum and Corculum in the family Cardiidae, and the other composed of the genera Tridacna and Hippopus in the family Tridacnidae. However, present results indicate that the azooxanthellate clams analyzed (Vasticardium flavum and Fulvia mutica) are more likely to form a clade with the species of Tridacna and Hippopus than with those of Fragum and Corculum. This topology suggests that either the symbiosis with zooxanthellae occurred independently in each of two lineages, Tridacna-Hippopus and Corculum-Fragum, or the symbiosis was established in clams ancestral to the lineages of both the zooxanthellate clams and the azooxanthellate clams Vasticardium and Fulvia, and the latter lost the symbiotic relationship after the symbiotic clam lineages had diverged.