The mechanisms that restrict gene flow between populations and facilitate population differentiation and speciation vary across the tree of life. In systems where physical barriers to gene flow are dynamic over time and space, such as many marine species, genetic introgression may be a major factor in the speciation process. In sympatric species of seabirds, hybridization has been frequently observed but few studies have investigated patterns of introgression. We used whole-genome sequence data to test for interspecific introgression between five pairs of tropical and subtropical seabird species and to test for gene flow within species across major land mass barriers and ocean basins. We found evidence for introgression between: blue-footed (Sula nebouxii) and Peruvian boobies (S. variegata); masked (S. dactylatra) and Nazca boobies (S. granti); and blue-footed and Nazca boobies. We found no evidence of introgression between blue-footed and brown boobies (S. leucogaster), or masked and brown boobies, despite observed hybridization between these species. We also found evidence for gene flow across several major land masses in three pantropical species: red-footed (S. sula), brown, and masked boobies. Finally, we report mixed evidence for ancient introgression between brown boobies and the ancestor of blue-footed, Peruvian, masked, and Nazca boobies. Our work indicates (1) that interspecific introgression has shaped contemporary booby diversity in the eastern Pacific, and (2) that contemporary physical barriers to gene flow between booby colonies are not absolute. Our findings contribute novel insights to the growing body of evidence that introgression is a widespread evolutionary process.