Understanding the connectivity among populations is a key research priority for species of conservation concern. Genetic tools are widely used for this purpose, but the results can be limited by the resolution of the genetic markers in relation to the species and geographic scale. Here, we investigate natal philopatry in green turtles (Chelonia mydas) from four rookeries within close geographic proximity (~ 200km) on the Mediterranean island of Cyprus. We genotyped hypervariable mtSTRs, a mtDNA control region sequence (CR) and 13 microsatellite loci to genetically characterise 479 green turtles using markers with different modes of inheritance. We demonstrated matrilineal stock structure for the first time among Mediterranean green turtle rookeries. This result contradicts previous regional assessments and supports a growing body of evidence that green turtles exhibit a more precise level of natal site fidelity than has commonly been recognised. The microsatellites detected weak male philopatry with significant stock structure among three of the six pairwise comparisons. The absence of Atlantic CR haplotypes and mtSTRs among these robust sample sizes reaffirm the reproductive isolation of Mediterranean green turtles and supports their status as a subpopulation. A power analysis effectively demonstrated that the mtDNA genetic markers previously employed to evaluate regional stock identity were confounded by an insufficient resolution considering the recent colonisation of this region. These findings improve the regional understanding of stock connectivity and illustrate the importance of using suitable genetic markers to define appropriate units for management and conservation.