In this study, the gametogenic cycle of the newly introduced Manila clam Ruditapes philippinarum was described for the first time for Turkish waters and compared with that of the native European grooved carpet shell clam Ruditapes decussatus coexisting in Cardak Lagoon (Canakkale, Turkey) in the Dardanelles. A total of 480 individuals were sampled for each species between January and December 2011. Both species exhibited similar distinct seasonal changes in gonad activity and completed their gametogenic cycles. In both species, gonads advanced very fast after winter reaching ripe stage in April and May in the Manila clams and carpet shell clams, respectively. In Manila clams, spawning commenced in April and continued until October. In carpet shell clams, spawning started in May, but the main spawning event occurred in June and continued until July with a discontinuation in August and a marginal spawning taking place in September and possibly in October. Gonad index (GI) values were indicated similarities in gonad development between males and females of both species with apparent synchronism between sexes during early development, first maturation and early spawning until July. We report for the first time the reproduction of the Manila clam in Turkish waters and show that optimal conditions for gametogenesis and spawning exist for this exotic species from March until October in the Dardanelles. This information will be useful for clam fishery management especially in areas where carpet shell clam and the Manila clam are known to coexist.