Following deglaciation of the Cook Inlet region of Alaska approximately 16 000 years ago, anadromous threespine stickleback (Gasterosteus aculeatus) rapidly colonized emerging lakes and rivers forming resident, freshwater populations. Although the precise body shape of the ancestral marine population is unknown, marine sticklebacks sampled from both Pacific and Atlantic sites present remarkably little body shape variation among populations, which suggests that the morphology of any of the marine populations could be used to represent the ancestral phenotype. To infer the net evolutionary trajectories of body shape change in the Cook Inlet radiation, derived body shapes of lacustrine samples were compared to the presumptive, primitive body shape, represented by the mean shape of two anadromous samples from Cook Inlet. In general, some derived body shape traits are shared by all freshwater populations but many traits evolved in opposite directions. The principal axes of shape variation among freshwater sample means were computed using Principal Components Analysis. The strong correlation between the direction of the principal component axes and lake habitat variables suggest that populations evolved toward selection peaks that are biased along the component axes due to biotic and abiotic features of the lakes.