The present study is considered as a preliminary experiment to generate new markers that include other segments along marine turtles' genome, as a tool to investigate new areas of variation/polymorphism between, among, and within populations and individuals. The PCR-based technique Sequence-Related Amplified Polymorphism (SRAP), best to our knowledge, was used for the first time to investigate the genetic polymorphism between and within Mediterranean and Red Sea green turtle (Chelonia mydas) populations. Based on the data obtained using twenty SRAP primer combinations, the polymorphism within the Mediterranean population was 73.8% while it reached 96% within the Red Sea population. Genotypic specific markers produced by SRAP for Mediterranean and Red Sea green turtle populations were 48 and 22 markers, respectively. The cluster analyses showed that the Mediterranean and Red Sea populations can be distinguished from each other into 2 completely different clusters. The similarity between individuals from Ras Muhammad Protected Area (PA), Hurghada, and some individuals from Zabargad showed distinguished and close relationships.  This study indicated that SRAP proved to be an easy and rapid method to investigate genetic variation between and within the Mediterranean and Red Sea marine turtles' populations.