Water frogs are one of the most interesting vertebrate groups, showing great diversity and complexity in their reproductive modes, ecology and evolutionary relationships, and with many cryptic species due to high morphological similarity. For many decades, a single species, Rana ridibunda, has been suggested to exist in Turkey. However, the application of new morphometric, molecular and bioacoustic techniques has recently revealed the occurrence of several distinct water frog taxa in Turkey. In this study, 340 bp long mtDNA ND3 region in 195 specimens was sequenced and subjected to phylogenetic analyses to detect geographical structure and species boundaries. Neighbor joining tree, minimum spanning network, SAMOVA and AMOVA were used to understand relationship within and among clades. Population demography was studied through mismatch distribution and neutrality tests. Results indicated that populations in southwestern Turkey show high diversity and strong geographic structuring. In Turkey there are four major maternal lineages, each probably representing a species: Thrace lineage represents Rana ridibunda Pallas 1771 in European Turkey / Ceyhan lineage indicates an unnamed taxon in Cilicia plain / South-central lineage occurs at the Lake District, Antalya, Konya and Karaman provinces and represents Rana caralitana Arikan, 1988 / Anatoliaca lineage (occuring in Asiatic Turkey except for central southern Turkey, Rhodes &amp / Karpathos, northeastern Syria, and probably also Iraq and Transcaucasia) is designated either as Rana cerigensis Beerli, Hotz, Tunner, Heppich, and Uzzell 1994 or as a new subspecies of R. caralitana, based on the degree of reproductive isolation present between the last two lineages.