The deep sea protobranch bivalve species Ledella pustulosa recently has been described as comprised of four subspecies, differentiated on subtle and qualitative differences in shell morphology. Two of these, L. p. pustulosa and L. p. marshalli, possess overlapping geographic distributions, L. p. pustulosa occurring on the continental slope, and L. p. marshalli occurring on the continental rise and at upper abyssal depths. Principal components analysis was applied to six samples of Ledella pustulosa from the Rockall Trough in order to explore patterns of variation in shell shape and to test whether the variability follows a depth-related cline which might be under environmental control. Two of these samples had previously been identified as L. p. pustulosa and L. p. marshalli, respectively. The distributions of shapes at every depth overlapped broadly with the distributions from other depths and none of the depths had uniformly distinct shells. However, the mean shapes of the six samples divided into two clusters: a shallow cluster characterized by a lower dorsal profile (smaller ‘shoulders’) and a deep cluster with larger ‘shoulders’. No bathymetric cline in shape was found within these clusters. A discriminant function based on training samples of L. p. pustulosa and L. p. marshalli correctly identified 84% of the shells in the training samples and was applicable over a wide range in shell size. It showed that the subspecies differed primarily in the dorsal profile. The discriminant function was applied to 598 shells from depths of 1632–2900 m in the Rockall Trough in order to test the hypothesis of depth-related segregation of the subspecies. Although individual variability was high, the results indicated a gradual transition from L. p. pustulosa dominance at ∼2000 m to L. p. marshalli dominance at 3000 m depth, but not marked segregation. A sample from 1632 m depth with large proportions of both subspecies disrupted the bathymetric trend and suggested a latitudinal gradient in distribution. Possible environmental factors, including bottom currents, acting on a common genotype to cause the observed pattern of differentiation, are also discussed.