Ceratophyllum tanaiticum Sapjegin, a species new to the flora of Hungary, was discovered at two localities in the Hungarian part of the Drava Plain in 2008. These are the westernmost, disjunct localities of this Pontic-Caspian endemic species. For characterization of the Hungarian specimens, nine morphological features of nine Ceratophyllum taxa were used in PCA, CVA analyses and UPGMA classification. In these analyses Hungarian and other C. tanaiticum samples always formed a cluster distinct from other Ceratophyllum taxa. These results confirm an earlier concept in which the character peduncle length contributed the highest loading value for separating C. tanaiticum from other 3–4 leaf-ordered species. Microscopic morphological features, including the number of longitudinally arranged lacunae in one row of parenchymatic tissue between the first and the second dichotomic branching, the length of the sequence between the first and second branching of leaves; number, morphology and width of bracts under the fruit of fresh Hungarian material are identified as new characters for C. tanaiticum, C. submersum and C. demersum.