The family Potamogetonaceae has been taxonomically re-evaluated in Turkey, employing traditional morphological as well as molecular approaches (rbcL, ITS). Our fieldwork, herbarium studies and molecular analyses proved the existence of 22 taxa, of which 18 belong to Potamogeton (including 4 interspecific hybrids), 3 to Stuckenia and 1 to monotypic Groenlandia. Morphological re-descriptions of the recognized taxa were prepared, and the information concerning their distribution in Turkey was refined, based on plant material from extensive fieldwork and on specimens stored in herbaria that were previously not examined. Additionally, new identification keys to genera and species, and distribution maps of the species were prepared. Phylogenetic relationships and intraspecific variations were assessed by including samples from other regions. The status of the Zannichelliaceae was investigated using nuclear and chloroplast DNA markers. Our results from ITS sequence divergence corroborate the separation of the two families noted by some authors, and are in accordance with the substantial morphological differences between them. Relatively large genetic distance and non-monophyly indicate that two genotypes of P. gramineus constitute cryptic species, for which the Turkish localities expand upon the previously known distribution areas. We identified P. schweinfurthii as a new species for Turkey and report P. ×angustifolius for the first time for this country. Weak morphological differentiation and high sequence similarity did not permit reliable differentiation between the closely related Stuckenia amblyphylla and S. filiformis.