The water frog form caralitana was first described as a subspecies of Rana ridibunda by Arikan (1988) from southwestern Turkey. Its orange ventral colour has been used as a diagnostic character since its description. After testing for a correlation between body size and ventral colour, we compared mtDNA and venter colour of adult specimens from 27 localities to assess the validity of this character for systematics of Anatolian water frogs. We mapped the distribution of each category and tested whether there is concordance between mtDNA haplotype and ventral colour of sampled individuals at the watershed level. Furthermore, we analyzed relationships between ventral colour and altitude. Size and ventral colouration were found to be significantly correlated. The distribution of orange ventral colour exhibited a complex clinal variation especially west of the Lake District where different coloured individuals are seen syntopically. In other regions, there were abrupt changes, presumably because of geographic barriers such as mountains. Our results indicate that although there is significant concordance between caralitana-specific mtDNA and orange venter colour, there are certain watersheds where the majority of sampled individuals exhibits discordance in mtDNA and ventral colouration. In all periphery regions, some degree of genetic introgression is indicated. These patterns clearly indicate gene flow between the caralitana lineage and non-caralitana lineages and is supported by lack of evidence for habitat-specific selection, the assignment of individuals from the same population into distinct clades, and the occurrence of an intermediate character between different forms in transition zones.