The alien bivalve Ruditapes philippinarum (Manila clam) was intentionally introduced along the Italian Coast of the northwestern Adriatic Sea for aquaculture purposes in 1983. In February 2013, R. philippinarum was recorded at a site of the northeastern Adriatic Sea (Zelena Laguna, vicinity of city Poreč, west Istrian Coast, Croatia). This finding represents the first record of R. philippinarum in Croatian waters. The colonized site is located at a distance of approximately 100 km by a straight line in the west east direction from the site where the mollusc was firstly introduced. At Zelena Laguna, R. philippinarum colonized the intertidal sandy substrate together with the native species Ruditapes decussatus. The two sympatric species were initially differentiated based on the morphology of the siphons. Molecular analysis of 16S rRNA gene confirmed the morphological distinction between the two species. Although the two species are very similar in shell morphology, the relationships width/length and width/height were negative allometric for R. decussatus and isometric for R. philippinarum. The relationship height/length was isometric for both species. Additionally, the length of the pallial sinus was significantly different between the two species (P < 0.001).