This paper assessed the systematic position of the genus Gomphogyne. The nuclear ITS, the chloro-plast rpl16, and trnS-trnR sequences were used to reconstruct the phylogeny of Gomphogyne and its related gen-era. Analyses of three separate and combined datasets provided a good amount of informative characters and re-solved the systematical relationships of Gomphogyne well. The maximum parsimony analyses revealed that: (1) Gomphogyne was a natural genus and was different from the genera Hemsleya and Gynostemma; (2) Hemsleya delavayi and H. macrocarpa did not belong to the genus Gomphogyne, but to the genus Hemsleya; and (3) Gomphogyne was sister to Hemsleya. It was assured that Gomphogyne was a monotypic genus. These results were largely in agreement with the systems of classification of the Cucurbitaceae of Jeffrey in 1990 and in 2005 and with that of Li for Hemsleya in 1993, but were different from the previous studies in which Gomphogyne and Gy-nostemma together were suggested to be sister to Hemsleya.