We investigated the extent of sexual dimorphism in body shape in adult threespine stickleback (Gasterosteus aculeatus) from 39 lakes, eight streams, and five marine (two brackish, three full marine) localities on the Haida Gwaii archipelago off the mid-coast of British Columbia, as well as three lakes from southern British Columbia with benthic–limnetic species pairs. Based on digital images of 709 males and 593 females, body shape was quantified using discriminant function analysis on partial warp scores generated from twelve homologous landmarks. All populations showed males with higher positive values for canonical vector 1, which are characterized by larger heads, larger gape, posteriad dorsal spines, posteriad pelvis, longer anal fin, and deep posterior caudal depth relative to those in females. Geographical variability was present, with the highest dimorphism occurring in two of the marine habitats in addition to large lakes, whereas reduced dimorphism occurs in small shallow dystrophic ponds. We suggest that this reduction is the derived condition and is primarily due to loss of niche breadth and convergence in body shape between the sexes in pond habitats. Analyses of two experimental pond populations indicate that up to 15% of the shape dimorphism can be attributed to habitat-induced phenotypic plasticity. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 505–516.