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The oceans are harsh environments where insects are not expected to thrive, yet a few skaters of the genus Halobates Eschscholtz, 1822 (Hemiptera: Heteroptera: Gerridae) have completely adapted to life on the open seas. There are five oceanic Halobates species that have well-established and distinct distributions, but little is known about their population dynamics and intraspecific genetic variation. Moreover, existing knowledge on most species has been largely based on limited sample sizes. We examined the phylogeographic patterns and inferred past population dynamics of three Halobates species (H. micans Eschscholtz, 1822, H. sobrinus White, 1883 and H. splendens Witlaczil, 1886) based on an unprecedented large number of specimens (73–199 individuals each) collected from the Eastern Tropical Pacific (ETP) Ocean. These species have distinct biogeographies, with H. sobrinus occurring mostly along coastal Mexico, H. micans in the ETP north of the equator, and H. splendens largely south of the equator in the cold tongue of water derived from the Peru (Humboldt) current. We did not find evidence for sub-population structure within each species over distances as far as 6000–7000 km. Populations of all three species were found to deviate from neutrality, with evidence of past population growth. Genetic diversity and haplotype genealogies varied between species, implying distinct evolutionary trajectories. Coalescent analyses using Bayesian skyline plots suggested that H. splendens underwent a population expansion ~ 1 Ma, whereas H. sobrinus and H. micans experienced demographic growth ~ 120 Ka to 100 Ka, respectively. The period of population expansion of H. splendens roughly corresponds to the establishment of cool, productive waters in the cold tongue starting ~ 1 Ma and reaching modern temperatures ~ 800 Ka. Population expansions of both H. micans and H. sobrinus north of the equator occurred mostly during the last interglacial period, characterized by increased frequency and dominance of El Niño conditions, and a relatively southerly position of the Intertropical Convergence Zone of high rainfall. Intensification of El Niño conditions between ~ 75 and 125 Ka may have produced a warmer, low wind and nutrient-depleted habitat favoring population growth for both H. micans and H. sobrinus. Key insights drawn from the results of this study, alongside future resolution of evolutionary relationships among Halobates species, will complete our understanding of how these remarkable insects conquered the high seas where no other insect could. [ABSTRACT FROM AUTHOR]