Although there have been several studies based on the molecular data of green toads, some ambiguities related to the systematics of these toads in Turkey still remain. Thus, we used combined mitochondrial genes (D-loop and 12S ribosomal RNA) to resolve these taxonomic problems. We also applied demographic analysis to elucidate the evolutionary history using these genes. We found 3 haplotype groups: 1 for Bufo viridis and 2 lineages for Bufotes variabilis, with only the latter represented in Turkey. This study showed a genetic diversity within Anatolian B. variabilis. Population genetic analysis of mismatch distributions, Tajima's D-statistic, and Fu's Fs test are consistent with a range expansion of the Bufotes variabilis group covering western Turkey. B. variabilis populations of lineage 1 and lineage 2, from western and eastern Anatolia respectively, are genetically identical. Mitochondrial DNA haplotype groups may reflect historical separation within B. variabilis. Our study indicated that allopatric distribution of B. variabilis within Anatolia occurred due to climatic shifts during the Pliocene. This study shows that Anatolia likely has served as a factor in vicariant species formation.