Biological interaction is one of the major agents maintaining the spatial heterogeneity of an organism distribution. Focusing on the less studied estuarine benthic system, we elucidate the fragmented distribution of the Manila clam and its causality. The distribution of the clam was restricted in a coastal shallow zone where dissolved oxygen was relatively rich. However, even in the shallow zone, the clam density was highly variable spatially, and was significantly reduced in the Asian mussel-dominate area. The field experiment detected that the spatial heterogeneity was due to a sediment hypoxia caused by the mussel coverage. The results can explain the mechanism why the mussel inhibits the clam’s survival, but not be a reason why the clam’s distribution is fragmented. Therefore, other mechanism(s) might function. Previous studies illustrated that the predation by diving-ducks drastically reduced the mussel biomass in winter, thus the duck predation is assumed to provide the mussel-free habitat for the clam. These suggest that the interactive effect by the Asian mussel and diving-ducks is one of the major causes of the Manila clam’s fragmented distribution.