A combined study of morphology, stem anatomy and DNA sequencing data (nuclear ribosomal ITS region and rpl32-trnL and rps12-rpl20 intergenic spacers of chloroplast DNA) was used to identify a putative Potamogeton hybrid from a river in NE Poland. Based on the morphological and anatomical characters the plants were tentatively identified as P. ×subobtusus Hagstr., a hybrid between P. alpinus Balb. and P. nodosus Poir. This identification was independently confirmed by the presence in hybrid individuals of an additive ITS sequence pattern from these two parental species. In all plants peaks corresponding to nucleotide states of both parents were clearly distinguishable, however the variants from P. nodosus dominated over those from P. alpinus. P. nodosus was also identified as the maternal parent of the hybrid based on cpDNA data and dominated the expression of morphological features in hybrid individuals. A detailed morphological description of P. × subobtusus and the typification of the name are provided. As P. nodosus rarely hybridizes with other species, existence of other hybrids, as well as possible difficulties in recognizing these taxa are also discussed.