This study investigated concentration of heavy metals, intersexuality and histological alterations of digestive gland in Ruditapes philippinarum. Samples were collected from three areas of Gamak Bay in May, 2010. The concentration of trace metals showed that Al was highest, Zn was second high concentration and the lowest concentration was Cd. The intersexuality was 18.5% and female was higher than the male. Intersex type was observed one types. Destruction of digestive tubule epithelium was highest among other biomarkers in digestive gland. Distribution of basophilic cell was 5.8% and lipofuscin was 1.8%.