A new fossil species of the pond snails (family Lymnaeidae Rafinesque, 1815), Lymnaea bogatschevi sp. n., from the Neogene (Khersonian–Maeotian transition) of southern Russia is described. It is characterized by a peculiar structure of the shell suture not found elsewhere in the family Lymnaeidae (both in living and extinct taxa). The suture of L. bogatschevi sp. n. may be described as a narrow groove that penetrates deep into the shell matter. This feature is developed both in protoconch and teleoconch whorls and is presented in several hundreds of specimens that precludes its origin as an individual abnormality. There are no environmental factors known to induce such groove-like sutures in aquatic pulmonates indicating a genetic basis for this structure in L. bogatschevi. Also, we report a single shell with the similar channelled suture from a sample of Lymnaea megarensis (Gaudry in Fischer, 1867) from the Pliocene of Greece. It seems, in this species the groove-like suture was represented as a rare individual aberration, and later this trait disappeared completely from the lymnaeid morphological repertoir. A possible phylogenetic relationships between L. bogatschevi and the recent L. (Kazakhlymnaea) taurica (Clessin, 1880) are suggested and briefly discussed.