Sexual dimorphism is understood as the result of sexual selection, ecological differentiation between the sexes, or a combination of both. Sexual variation is subject to the uniform genetic architecture controlling sexually homologous traits. This interplay may both constrain the evolution of this variation and provide a pathway to speciation and intraspecific diversity. Describing sexual variation as “dimorphism” overly simplifies the mosaic nature of the effects of selective pressures on organisms. Not all traits in a species display sexual variation and when variation exists in multiple phenotypic traits, it is often non-uniform. Moreover, selection driving sexual variation influences phenotypic variation not directly associated with genotypic sex. This important component of phenotypic variation is often lost in discussions focusing solely on a statistically significant binary. Threespine stickleback (Gasterosteus aculeatus)display rapid adaptive responses and sexual variation in several phenotypic traits, ranging from body size to cranial shape. The presence, magnitude and direction of sexual variation in these traits varies greatly both within and across habitats. Using 3D geometric morphometrics, we quantified shape and size of the cranial, pectoral and pelvic regions of sticklebacks in marine and freshwater habitats from southwestern B.C. We show varying degrees of sexual variation in body regions, in habitats, within sex, and habitat-dependent modulation of sex effects on morphology.