Genetic structure of Chelonia mydas in the nesting beaches of Turkey and Northern Cyprus was analyzed using mitochondrial DNA control region and nuclear DNA. Tissue samples were collected from 256 different nests located on six nesting beaches. Sequencing of 859 bp fragment of control region revealed six distinct mtDNA haplotypes of which three were described for the first time in this study. Haplotype CM-A13 was the major one uncounted for 97.3% and others were differed by one substitution. Low level of mtDNA variation in green turtle across the study area makes it impractical for determination of genetic structuring of nesting aggregates and female philopatry. Findings from this study showed higher genetic variation and structuring in nDNA than mtDNA among the Mediterranean nesting aggregates. Analysis of microsatellite data of the Mediterranean green turtle revealed sufficient amount of genetic variation suggesting each nesting colony as a management unit. (C) 2012 Elsevier Ltd. All rights reserved.