For improved resource management, we estimated the genetic structure of the asari clam Ruditapes philippinarum to reveal the local population network formed by transportation of pelagic larvae in Ise Bay, Japan. We sampled juvenile clams (shell length < 20 mm) at six locations in Ise Bay and one location in the adjacent Mikawa Bay in May and November in 2013 and 2014. We analyzed 24 or 25 individuals from each sampling location at each sampling period and performed microsatellite analysis with 4 loci (Asari16, Asari62, Asari64 and KTp8). Analysis of molecular variance (AMOVA) revealed significant genetic differentiation between the sampling periods (FCT = 0.00590, P = 0.00000) but no genetic differentiation between the sampling locations (FCT = -0.00142, P = 0.83773). This indicates that the genetic characteristics of settlements are nearly homogeneous for different sampling periods but not so for different locations. It is thus possible that pelagic larvae originate from multiple sites in the bays and are intermingled, which suggests a metapopulation may have formed by transportation of pelagic larvae in Ise Bay.