The three known sympatric Biomphalaria species that occur in Lake Albert; B. choanomphala, B. stanleyi and B. sudanica, were studied using both molecular (COI, 16S and ITS) and shell morphometric data. An unidentified sample of 18 Biomphalaria specimens from Lake Albert were divided in three morphotypes according to aperture height and coiling rate and subsequently identified through molecular inferences and morphometry. The 18 specimens were identified as follows; six specimens were identified as B. sudanica, seven species as B. stanleyi, four as B. cf. choanomphala and a single specimen as B. pfeifferi. The latter was inferred with strong molecular support only, since it had similar shell morphology to typical B. stanleyi snails, thus it might be an ecophenotypic form of B. pfeifferi adapted to a lacustrine environment. Biomphalaria stanleyi exists in forms that resemble B. choanomphala, and B. choanomphala has further overlap in morphology with B. smithi. However, the results showed some disagreement between molecular and morphometric identification, hence making it difficult to rely on shell morphology alone in identification. Overall the morphometric analysis divided Biomphalaria in two possible ecophenotypes i.e. a lacustrine type with rapidly increasing whorls and relatively high apertures and a non-lacustrine type (including snails inhabiting lake edges) with slowly increasing whorls and low apertures.