Ecological and biogeographic information for marine gastropods has lagged behind taxonomic, molecular and phylogenetic information, limiting understanding of evolutionary processes. We investigated niche separation and speciation in rapinine whelks that represent a rare deep estuarine penetration by muricid gastropods. We studied the genetic and ecological differentiation of four Indothais morphotypes, distributed along a salinity gradient in Brunei (Borneo, South East Asia). Our molecular analyses, based on three mitochondrial genes (COI, 12S rRNA and 16S rRNA) and one nuclear gene (28S rRNA), revealed three species having the following relationship [Indothais rufotincta (Tan & Sigurdsson, 1996), [I. javanica (Philippi, 1848), [I. gradata (Jonas, 1846)]]]. This pattern coincided with their salinity-related distributions, such that I. rufotincta occurred alone in the open coastal waters, and I. javanica and I. gradata extended into the upper estuary. This suggests speciation through divergent selection and local adaptation, specifically synapomorphic low salinity tolerance by I. javanica and I. gradata. The observed intertidal vertical separation where the species co-occur suggests competitive exclusion of the others by the most-recently evolved I. gradata. This species also showed greatest morphological and genetic variation, and unique niche expansion involving feeding on both hard surface and muddy sediment organisms. Our study presents a novel hypothesis for the speciation of these snails.