Giant clams (Tridanidae) are one of the high value marine mollusks in Vietnam. A total of 4 species were collected along Vietnamese coast (Vân Phong Bay and Con Dao Island). Bayesian Inference, Maximum Parsimony and Maximum Likelihood tree were constructed based on different mitochondrial genetic molecular marker, 16S  and CO1 mtDNA gene from T. crocea, T. squamosa, T. maxima, Tridacna sp., and several sequences derived from Genbank. The results from 16S mtDNA showed that giant clams formed 2 monophyletic groups following genus Hippopus and Tridacna. Within Tridacna group, T. crocea was more closely related to T. squamosa than to T. maxima. .T. maxima was closed to T. costata and Tridacna spYCY2005.  T. gigas was clustered to T. derasa. T. crocea and T. squamosa were sister taxa and sister group to T. maxima and T. costata. They together formed a sister clade to T. gigas and T. derasa. Two species of genus Hippopus (H. hippopus và H. porcellanus) clustered together with high bootstrap support. The analysis based on CO1 mtDNA showed the relationships as ((T. squamosa+T. crocea) (Tridacna sp.)) (T. maxima+T. gigas). T. derasa has undetermined taxonomic position.