Two terrapin subspecies are currently considered Seychelles endemisms and Critically Endangered according to IUCN criteria, with several conservation measures having been proposed and actively initiated in the recent years. We use molecular data to examine their population diversity and structure across the archipelago and find a complete lack of variation at the mtDNA level. This can be explained by the strong founder effect associated with island colonisation, allied to the low evolution rate described for turtle mtDNA. However, a very recent arrival of Seychellois terrapins to the archipelago by human action cannot be discarded. The use of highly variable markers such as microsatellites and the clarification of their (native or not) status is therefore essential and should be implemented as an urgent priority in species management plans. Some differentiation between the Seychellois and Malagasy P. castanoides is observed but should be taken carefully until geographically broad level sampling across Madagascar is available.