Giant clams in Singapore have been subjected to anthropogenic impacts such as fishing, coastal development and sediment pollution for decades, making their study a priority for local reef management. Between September 2009 and August 2010, 29 reefs among Singapore’s Southern Islands were surveyed (total area = 87515 m2). Both intertidal and subtidal zones were included, i.e. from shore to the edge of the upper reef slope (depths = 1 to 6 m). A total of 59 clams (but no juveniles) were found, resulting in a contemporary density of 0.067 per 100 m2. Only 2 species, Tridacna crocea and T. squamosa, were encountered, compared to the 4 species recorded historically. The genetic relatedness among individuals from these 2 species was examined using cytochrome c oxidase subunit I (COI). Higher levels of polymorphism and genetic diversity were observed among T. crocea; both were less pronounced in the T. squamosa population, where a single haplotype was present in half of the individuals. The reef conditions in Singapore, especially the lack of suitable substrate and high turbidity, create a poor environment for giant clam reproduction and recruitment. It appears to be low mortality among mature clams that maintains the present population, but with the adults exposed to ongoing stressors, Singapore’s entire giant clam stock is endangered.