Potamogeton is a genus well known for the occurrence of interspecific hybrids. The linear-leaved Potamogeton species commonly have highly variable morphological characteristics. Their hybrids often show the similar vegetative characters of their parental species. Their identification based solely on morphology is not always conclusive. In order to clarify whether there existed any hybrids from the linear-leaved Potamogeton plants collected in China, we used internal transcribed spacers (ITS) of nuclear ribosomal DNA and chloroplast rbcL gene sequences to identify the hybrids. Using ITS sequence additivity, we identified four hybrids, P. orientalis (P. pusillus ×P. oxyphyllus), P. pusillus × P. berchtoldii, P. foliosus × P. octandrus, and P. cristatus ×P. octandrus. The latter three hybrids should be considered as new hybrids in Potamogeton. The maternal parents of the four hybrids were confirmed by chloroplast rbcL gene sequence.