The Magnificent Frigatebird (Fregata magnificens) is a monogamous, widespread, neotropical, pelagic seabird with low flight costs, high dispersal capacity, sex-biased dispersal, and female mate choice. Here, we adopt an integrative approach to evaluate the influence of behavior, male-biased philopatry, female choice, and geographic distance as non-physical barriers to dispersal acting on the genetic structure of magnificent frigatebirds in the 4 largest Mexican breeding colonies. We integrate ecological dispersal observations from tagging studies, analyses of maternally and biparentally inherited genetic markers, and group-structured population modeling. Mitochondrial DNA (matrilineal) and randomly amplified polymorphic DNA (biparental) data provided evidence of genetic differentiation between ocean basins, as well as among Eastern Pacific breeding colonies, and absence of a genetic pattern of isolation by distance. Our ecological, genetic, and modeling results are concordant with the expected effects of sex-biased philopatry and female mate choice as non-physical barriers to interbreeding, and suggest that geographic distance does not play a significant role in the genetic distinction of breeding colonies. The genetic differentiation found between Eastern Pacific and Caribbean, as well as that among Eastern Pacific breeding colonies is of consequence for the management plans and conservation measures of the Magnificent Frigatebird in the region.