Micro-evolutionary processes that underpin genetic and morphological variation in highly mobile pelagic vertebrates are virtually unknown. Previous findings preferentially invoke vicariant isolation due to large-scale physical barriers such as continental landmasses, followed by genetic drift. However increasingly, evidence for divergence by non-random processes (e.g. selection, plasticity) is being presented. Wedge-tailed shearwaters are wide-ranging seabirds with breeding colonies located such that they experience a variety of environmental pressures and conditions. Previous work on this species has provided evidence of inter-colony divergence of adult morphology and foraging modes, as well as chick developmental patterns, suggesting that reinforcement among colonies is possible. In order to evaluate the micro-evolutionary processes driving this observed variation, our study compared patterns of gene flow with morphological and environmental variation among four colonies of wedge-tailed shearwater breeding within the Indo-Pacific Ocean basin. Estimates of gene flow differed according to the genetic marker used; most likely, this is a function of different mutation rates. Nuclear introns suggest that gene flow among wedge-tailed shearwater breeding colonies within the Indo-Pacific Ocean basin is substantial, however microsatellite markers imply that gene flow is reduced. In general, levels of genetic divergence were relatively low and did not correlate with geographic distance, morphological distance or environmental differences (sea-surface temperature and chlorophyll a concentration) among colonies. We suggest that genetic drift alone is unlikely to be the major source of morphological variation seen in this species. Instead, we propose that non-random processes (selection, plasticity) underpin morphological diversity seen in this and possibly other seabird species.