The present study reports on population structure analysis of the marbled crab Pachygrapsus marmoratus(Fabricius, 1787) from the Tunisian coast, an appropriate location to study biogeographical processes because of the presence of a well-known discontinuous biogeographic area(the Siculo-Tunisian Strait). Patterns of morphological and genetic variation of this highly dispersive and continuously distributed decapod species were assessed among its geographically close populations which cover almost the entire Tunisian coastline. A total of386 specimens from nine sites were collected and examined for morphometric variability at 14 morphometric traits. The results of multivariate analyses of linear morphometric traits showed the existence of sexual dimorphism in this species by PERMANOVA(Permutational multivariate analysis of variance). In addition, both CDA(Canonical discriminant analysis) and NPMANOVA(Non parametric MANOVA test) analyses revealed statistically significant differences among the studied locations for both sexes. Overall, the outcome of CDA analysis showed that over 87% of individuals could be assigned correctly to three regional groups in both sexes(North, Center and South). Specifically, SIMPER(Similarity Percentages) analysis showed that carapace length,carapace width and merus length were major contributors to the morphometric separation between populations.The pattern of phenotypic variation suggested by morphometric analyses was found to be highly discordant with that suggested by the analysis of a mitochondrial marker(cytochrome oxidase I, COI). Indeed, the results inferred from restriction fragment analysis of the COI in 180 crabs, suggested high genetic homogeneity. Very low levels of haplotype diversity(h) were found in almost all the studied populations, associated with non significant genetic distances for nearly all population comparisons. Explanations to these morphometric and mt DNA patterns as well as the discrepancy between them are discussed. The present study reports on population structure analysis of the marbled crab Pachygrapsus marmoratus (Fabricius, 1787) from the Tunisian coast, an appropriate location to study biogeographical processes because of the presence of a well-known discontinuous biogeographic area (the Siculo-Tunisian Strait) . Patterns of morphological and genetic variation of this highly dispersive and continuously distributed decapod species were assessed among its geographically close tags. Which cover almost the entire Tunisian coastline. A total of 386 specimens from nine sites were collected and examined for morphometric variability at 14 morphometric traits. The results of multivariate analyzes of linear morphometric traits showed the existence of sexual dimorphism in this species by PERMANOVA (Permutational multivariate analysis of variance). In addition, both CDA (Canonical discriminant analysis) and NPMANOVA (Non parametric MANOVA test) differences amon Overall, the outcome of CDA analysis showed that over 87% of individuals could be assigned correctly to three regional groups in both sexes (North, Center and South). Specifically, SIMPER (Similarity Percentages) showed showed that carapace length was, carapace width and merus length were major contributors to the morphometric separation between populations. The pattern of phenotypic variation suggested by morphometric analyzes found to be highly discordant with that suggested by the analysis of a mitochondrial marker (cytochrome oxidase I, COI ). Indeed, the results inferred from restriction fragment analysis of the COI in 180 crabs, suggested high genetic homogeneity. Very low levels of haplotype diversity (h) were found in almost all the studied populations, associated with non significant genetic distances for nearly all population comparisons. Explanations to these morphometric and mt DNA patterns as well as the discrepancy between them are discussed.