Water frogs of the genus Pelophylax Fitzinger, 1843 are one the most frequently studied frog species in Europe but are relatively poorly explored in the Balkan Peninsula and Croatia. Different species hybridize and produce fertile offspring, which is a rare phenomenon in the animal world. This study was conducted to gain a better insight into the presence of Pelophylax species and hybrids in Croatia. Croatia is a natural habitat of the Pool frog and the Marsh frog, Pelophylax lessonae and Pelophylax ridibundus and their fertile hybrids, Pelophylax kl. esculentus, but recent research has also determined the presence of Pelophylax kurtmuelleri and Pelophylax shqipericus. Water frogs are highly variable species by morphological and morphometric characteristics, therefore molecular-phylogenetic methods are used for more accurate determination. Replicated fragments of SAI-1 nuclear DNA markers were used to determine the species or the hybrid, whereas replicated COI fragments of the mitochondrial DNA were used to determine the maternal line of the analyzed individuals. Based on the nuclear and mitochondrial DNA, the analyzed frogs from seven localities, four in continental Croatia (Zagreb, Međimurje, Crna Mlaka 1, Crna Mlaka 2), two in Dalmatia (Otrić and Biskupija) and one in Lika (Podlapačko polje) represent a very diverse group characterized by high levels of hybridization and introgression. Most frogs from this research have genes of several frog species. The morphological features that have proved to be the most significant in determination are the coloring of the hips and legs, the length of the leg and the shape and size of the metatarsal tubercle.