AbstractAimDrivers of extant population genetic structure include past climate‐driven range shifts and vicariant events, as well as gene flow mediated by dispersal and habitat continuity. Their integration as alternative or complementary drivers is often missing or incomplete, potentially overlooking relevant processes and time scales. Here we ask whether it is the imprint of past range shifts or habitat connectivity driven by oceanographic transport that best explain genetic structure in a poorly understood model, a forest‐forming African kelp.LocationSouthwestern coast of Africa (Benguela current region).TaxonLaminaria pallida.MethodsWe estimated genetic variability along the species distributional range using 14 microsatellite markers. This genetic variability was compared to estimates of past range shifts derived from species distribution modelling for the Last Glacial Maximum (LGM), the mid‐Holocene (MH) and the present, and estimates of habitat connectivity derived from oceanographic biophysical modelling.ResultsThe species is structured in two clusters, a southern cluster with much richer (allelic richness A: 10.40 ± 0.33) and unique (private alleles PA: 56.69 ± 4.05) genetic diversity, and a northern cluster (A: 4.75 ± 0.17; PA: 6.70 ± 1.45). These clusters matched well‐known biogeographical regions and their transition coincided with a dispersal barrier formed by upwelled offshore transport. No major range shifts or vicariant events were hindcasted along the present range, suggesting population stability from the LGM to the present.Main conclusionsHabitat connectivity, rather than past range shifts, explains the extant population structure. Future environmental requirements of the species along the Benguela upwelling system are projected to persist or even intensify, likely preserving the observed genetic patterns for the years to come. Yet, the differentiation and endemicity between clusters, and the isolation structured by the regional oceanography, implies high conservation value for genetic biodiversity, and even more if considering the ecological, social and economic services provided by kelp forests.