The recognition of hybrids of linear-leaved taxa of Potamogeton (sect. Graminifolii;) based on morphology is difficult and often debatable. As a consequence, currently only a few hybrid taxa are considered valid and many linear-leaved hybrids described in the past are not now recognized. On the other hand, the use of molecular tools has recently allowed more efficient tests of the origin of morphological forms and the tracking of hybridization events in Potamogeton systematics. In this paper, Potamogeton ×maëmetsiae Zalewska-Gałosz et M. Ronikier nothosp. nov. (Potamogetonaceae), a hybrid between two linear-leaved species, P. friesii and P. rutilus, is described and illustrated. Hybrid plants were collected from two Central-European populations growing in Lake Skaidrys (Lithuania) and Soitsjärv (Estonia). The hybrid origin of the new entity was identified based on a morphological survey and independently confirmed using nuclear (ITS, 5S-NTS) and chloroplast (rpl32-trnL intergenic spacer) DNA sequence data and AFLP analysis of genetic structure. Differences between P. ×maëmetsiae and similar taxa are outlined and other relevant details of the new hybrid discussed.