Genetic variation was investigated using allozymes, cytochrome c oxidase subunit I, internal transcribed spacer region 1, and microsatellite markers in mainland and insular populations of the carpet shell Ruditapes decussatus from the western and eastern Mediterranean Basin. Five morphometric parameters and weight of valves were also used to study the distribution of variation within and among populations. The species is characterized by a relatively high inter- and intrapopulation morphological and genetic variability. The highest values of percent polymorphism and heterozygosity (allozyme and microsatellite data) were found in the sample from Kerkennah Island. The occurrence of higher levels of genetic variability in insular population is probably because this population inhabit marginal environment characterized by temporal-ecological instability. The genetic heterogeneity analysis demonstrates a certain amount of genetic differentiation among local populations of R. decussatus with a relatively high level of genetic subdivision. Sample from Kerkennah Island was differentiated from almost all other populations. Kerkennah Island clams are also the most different in morphology. This study was intended to elucidate, from genetic markers and morphometric parameters, the relative importance of the biogeographical properties of islands on the observed patterns of differentiation of the Kerkennah population.