The purpose of this study was to provide basic data for evaluating the reproductive health of bivalves using intersexuality. We analyzed purplish bifurcate mussel Mytilisepta virgata (n = 67, shell height 37.1±8.3 mm), Manila clam Ruditapes philippinarum (n = 288, shell length 28.6±4.2 mm) collected from coastal water near Yeosu, Korea. The sex ratio (female:male) of M. virgata and R. philippinarum were 1:1.5 and 1:0.8, respectively, and showed differences depending on the collection area. The total intersexuality of M. virgata was 20.9%. The intersexuality in female (33.3%) was higher than in male (12.5%), and the regional intersexuality was 72.7% in Sogyeongdo, 20.0% in Oesamdo and 5.6% in Jungsamdo with the highest in Sogyeongdo. The total intersexuality of R. philippinarum was 11.8%. The intersexuality in female (17.5%) was higher than in male (4.7%), and regional intersexuality was 20.0% in Neungchodo, 13.0% in Dokdo, 2.8% in Samdo, 5.9% in Orando, 19.6% in Oesamdo with the highest in Neungchodo. The incidence of intersexuality according to distance from cities and ports each sampling area showed no clear tendency. Intersex specimens were showed histological structure changes of digestive gland, such as digestive tubule disruption and necrosis of epithelial cells, accumulation of eosinophilic granules in lumen of tubule, necrosis of connective tissue. These results suggest that not only the histological structure of the digestive gland but also intersexuality should be used as important biomarker for toxicity assessment of pollutants.