Kelp forests are declining in many regions globally with climatic perturbations causing shifts to alternate communities and significant ecological and economic loss. Range edge populations are often at most risk and are often only sustained through localised areas of upwelling or on deeper reefs. Here we document the loss of kelp forests (Ecklonia radiata) from the Sultanate of Oman, the only confirmed northern hemisphere population of this species. Contemporary surveys failed to find any kelp in its only known historical northern hemisphere location, Sadah on the Dhofar coast. Genetic analyses of historical herbarium specimens from Oman confirmed the species to be E. radiata and revealed the lost population contained a common CO1 haplotype found across South Africa, Australia and New Zealand suggesting it once established through rapid colonisation throughout its range. However, the Omani population also contained a haplotype that is found nowhere else in the extant southern hemisphere distribution of E. radiata. The loss of the Oman population could be due to significant increases in the Arabian Sea temperature over the past 40 years punctuated by suppression of coastal upwelling. Climate-mediated warming is threatening the persistence of temperate species and precipitating loss of unique genetic diversity at lower latitudes.

Aim Drivers 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. Location Southwestern coast of Africa (Benguela current region). Taxon Laminaria pallida. Methods We 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. Results The 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 conclusions Habitat 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.

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