Environmental gradients have been shown to disrupt gene flow in marine species, yet their influence in structuring populations at depth remains poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis) are demersal species co-occurring in the Benguela Current system, where decades of intense fishing resulted in severely depleted stocks. Previous studies identified conflicting mtDNA genetic sub-structuring patterns, and thus contrasting evolutionary trajectories for both species. Using ten microsatellite loci, the control region of mtDNA, and employing a seascape genetics approach, we investigated genetic connectivity and the impact of prolonged exploitation in two fish species, which are characterized by different patterns of fishing pressure. Three consecutive years were sampled covering the entire distribution (N = 2100 fishes). Despite large estimated population sizes, both species exhibited low levels of contemporary genetic diversity (0.581 < HE < 0.692), implying that fishing has had a significant impact on their genetic composition and evolutionary trajectories. Further, for Merluccius paradoxus, significant temporal, but not spatial, divergence points to the presence of genetic chaotic patchiness. In contrast, Merluccius capensis exhibited a clear latitudinal cline in genetic differentiation between Namibia and South Africa (FST = 0.064, P < 0.05), with low (0.2% per generation) estimates of contemporary gene flow. Seascape analyses reveal an association with bathymethry and upwelling events, suggesting that adaptation to local environmental conditions may drive genetic differentiation in M. capensis. Importantly, our results highlight the need for temporal sampling in disentangling the complex factors that impact population divergence in marine fish.
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