Background: Fejevarya limnocharis (Dicroglossidae) is found widespread in Peninsular Malaysia. We analyzed the mitochondrial DNA control region sequence data to evaluate the genetic variability and population structure of this species, based on 106 individuals from 14 populations in the west coast (northwest and central west) and two populations from the east coast of Peninsular Malaysia. Results: Of 519, 13 variable sites (six parsimony informative sites) were observed, defining 14 unique haplotypes. We found very low levels of genetic variability, with three of the 16 populations exhibiting total absence of genetic variation. Both phylogenetic analyses based on NJ and MP methods failed to detect any geographic structuring between the east and west coast (northwest and central west combined) populations.Conclusions: Consequently, it can be inferred that genetic structuring F. limnocharis populations in the Peninsular Malaysia was largely shaped by natural barriers. However, when this breaks down as between the central west and east peninsular regions, genetic differentiation is reduced. Further studies, with more efficient markers and larger populations, especially from the southern regions, are required to corroborate the findings.

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