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Background  Studying species with disjunct distributions allows biogeographers to evaluate factors controlling species ranges, limits on gene flow, and allopatric speciation. Here, we use phylogeographic and population genetic studies of the barnacle  Pollicipes elegans  to discriminate between two primary hypotheses about the origin of disjunct distributions of extra-tropical populations: trans-tropical stepping-stone colonization versus an out-of-the tropics origin.    Results  Nucleotide diversity peaked in the centre of the species’ range in samples from El Salvador and was lower in samples from higher latitudes at Mexico and Peru. Haplotypes from El Salvador samples also had a deeper coalescent, or an older time to a most recent common ancestor. A deep phylogeographical break exists between Mexico and all samples taken to the south (El Salvador and Peru). Isolation-with-migration analyses showed no significant gene flow between any of the three regions indicating that the difference in genetic differentiation among all three regions is explained primarily by differences in population separation times. Approximate Bayesian Computation model testing found strong support for an out-of-the tropics origin of extra-tropical populations in  P. elegans .    Conclusions  We found little evidence consistent with a stepping-stone history of trans-tropical colonization, but instead found strong evidence for a tropical origin model for the largely disjunct distribution of  P. elegans . Sea surface temperature and habitat suitability are likely mechanisms driving decline of populations in tropical regions, causing the disjunct distribution.    Electronic supplementary material  The online version of this article (doi:10.1186/s12983-015-0131-z) contains supplementary material, which is available to authorized users.

Out-of-the tropics or trans-tropical dispersal? The origins of the disjunct distribution of the gooseneck barnacle Pollicipes elegans