The viviparid genus Margarya Nevill, 1877 is endemic to China and has only been recorded from the lakes of the Yunnan Plateau. Currently, all recognized species of this genus have become threatened or even extinct due to water pollution and overharvesting. In the current paper, Margarya melanioides Nevill, 1877 and Margarya mansuyi Dautzenberg & Fischer, 1905 are re-described based on newly collected material from Lake Dianchi and Lake Xingyun respectively. Intraspecific morphological variability of the shell, especially with respect to the development of the spiral keel, was found to be great. M. melanioides and M. mansuyi can be easily distinguished from each other as well as from other congeners by their relative size, as well as the number and development of the spiral keels. Radulae of the two species are relatively uniform with little differentiation in the number and shape of the teeth.