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Abstract Aim To investigate how marine barriers shaped the demographic history of Atlantic seahorses (Syngnathidae: Hippocampus ). Location Atlantic Ocean. Methods Range‐wide sampling ( n = 390) at mitochondrial and up to five nuclear DNA loci was carried out across the Hippocampus erectus species complex ( H. erectus from the Caribbean/North America, H. patagonicus from South America and H. hippocampus from Europe and West Africa). Multi‐species coalescent and approximate Bayesian computation ( ABC ) frameworks were used to estimate support of competing biogeographical hypotheses and demographic parameters, including lineage divergence times, effective population sizes and magnitudes of population size change. Results We identified four distinct lineages within the H. erectus complex. A posterior probability of 0.626 and corresponding Bayes factors ranging from 3.68 to 11.38 gave moderate to strong support for a basal divergence between South American populations of H. patagonicus and Caribbean/North American populations of H. erectus coincident with the inter‐regional freshwater outflow of the Amazon River Barrier ( ARB ). Estimates of historical effective population sizes and divergence times indicate that European and West African populations of H. hippocampus expanded after colonization from a more demographically stable Caribbean/North American H. erectus . Main conclusions Our findings of trans‐Atlantic colonization followed by isolation across a deep oceanic divide, and isolation across a freshwater barrier, may demonstrate a contrast in marine divide permeability for this group of rafters. Demographic inference supports the establishment of an ancestral population of the H. erectus complex in the Americas, followed by the ARB splitting it into Caribbean/North and South American lineages at a time of increased sedimentation and outflow. Our estimates suggest that following this split, colonization occurred across the Atlantic via the Gulf Stream currents with subsequent trans‐Atlantic isolation. These results illustrate that rafting can be a means of range expansion over large distances, but may be insufficient for sustaining genetic connectivity across major barriers, thereby resulting in lineage divergence.