Genetic diversity within a species can be shaped by abiotic factors, such as climate and geography. We aimed to ascertain the relative importance of these two abiotic factors to Indrella ampulla, a monotypic snail species from the Western Ghats, India, that has three colour morphs with some overlapping distributions. We also wanted to investigate whether these colour morphs represent divergent lineages or incipient species. We sequenced one nuclear and two mitochondrial genes from 32 individuals of I. ampulla.We used phylogenetic, population genetic, and niche modelling tools to address these questions. The results suggested that the colour morphs were not reciprocally monophyletic and exhibited considerable niche overlap, suggesting that they cannot be considered as incipient species. Furthermore, the results showed that the impact of palaeoclimatic oscillations in shaping the genetic diversity of this species cannot be determined conclusively. The Palghat Gap seems to have shaped the genetic diversity in this group to a certain degree. The colour morph distributed south of the Palghat Gap did not show admixture and exhibited the least amount of niche overlap with the other morphs. The geography of the landscape seems to have played a prominent role in shaping genetic diversity in this species.