Variation in snail shell shape has provided evolutionary biologists with excellent material for the study of local adaptation to local environments. However, assuming shell shape variation is evidence of distinct lineages (species) may have led to taxonomic inflation within some gastropod lineages. Here we compare shell shape variation and genetic structure of two independent lineages of New Zealand rocky shore whelks in order to understand the process that lead to an unusual disjunct distribution. We examined the Buccinulum vittatum complex (three subspecies plus B. colensoi) using mitochondrial DNA sequences, 849 single nucleotide polymorphisms, and geometric morphometric data on shell shape. Specimens within the range of Buccinulum colensoi shared nuclear markers and mtDNA haplotypes with the southern subspecies B. vittatum littorinoides, while the northern samples (B. v. vittatum) had distinct genotypes. We infer that gene flow between B. colensoi and B. v. littorinoides is greater than between either of these taxa and B. v. vittatum. The distinctive shell sculpturing of B. colensoi is maintained despite gene flow, suggesting a role for selection. Although the shell form of B. colensoi appears to be an adaptation to local conditions we did not observe convergent evolution in the sympatric whelk species Cominella maculosa.