The clam Ruditapes decussatus (Linnaeus 1758) is an indigenous species in the Mediterranean Sea, so it also inhabits the eastern coast of the Adriatic Sea. In recent years, this species has been endangered by related species Ruditapes philippinarum (Adams & Reeve 1850), which was introduced into the Mediterranean Sea from Southeast Asia in the early 1980s. Due to invasiveness and good adaptability, R. philippinarum is spreading rapidly, threatening the native clam R. decussatus. The morphological similarity between R. decussatus and R. philippinarum as well as the presence of both species at the same habitats make their identification extremely difficult. In this paper, for the first time the species from the genus Ruditapes have been analyzed in the Croatian part of the Adriatic Sea by using molecular DNA markers. Analysis of one mitochondrial (16S rDNA) and three nuclear (5S rDNA, ITS1, ITS2) markers revealed the presence of non-native species R. philippinarum at Zelena Laguna in the vicinity of the city Poreč. This is the first record of invasive bivalve R. philippinarum in the Croatian part of Adriatic Sea. Analyses of R. decussatus and R. philippinarum samples from the Adriatic Sea did not discover their hybrids. However, the hybrids have been detected in the control group of samples originating from the Marmara Sea. Detection of hybrids has confirmed the advisability and effectiveness of the use of different DNA markers to identify Ruditapes species and their hybrids.