Giant clams are harvested by coastal communities around Savu Sea for food. As one of the important inhabitants of the reef, their status in terms of abundance of adult population and recruits was assessed. The genetic structure of Tridacna maxima was also determined for use in the establishment of network of MPAs around Savu Sea. There were four species identified during the survey: Tridacna crocea, T. maxima, T. squamosa and Hippopus hippopus with T. maxima as the most common in all sites. Clam density ranged from 0.33 ind./ m2 to 19 ind./ m2.175 Population subdivision was found to be highly significant among the five T. maxima populations as assessed using the Analysis of Molecular Variance (AMOVA). The percentage of total molecular variation within samples was 73.20%, and that among samples was 26.80%, amounting to FST = 0.26798 which is significant (p-value = 0.014). However, pairwise comparison revealed genetic relatedness between some populations.