Aim Although many studies have reported the effects of climate change on species' distributions, most of them consider each species as a physiologically homogenous unit. However, different lineages or populations inhabiting distinct bioregions within a species' distributional range can retain unique genetic diversity that could result in distinct adaptive capacities. A recent, large, climate‐correlated distributional range contraction occurred at the southern edge of the intertidal macroalga Fucus vesiculosus, causing loss of genetic diversity unique to the southern clade. We tested for differential selective constraints and signs of local adaptation to thermal stress in the two genetic lineages. Location Iberian Atlantic shores. Methods We performed a series of common garden experiments and a field reciprocal transplant. Results In the laboratory, southern F. vesiculosus showed higher resilience to heat stress than northern individuals. On the southwest coast of Portugal, local individuals grew more than those transplanted from the northern range; in the north of Portugal, growth rates did not differ significantly between lineages. Conclusions We present evidence for unique adaptive traits at the retreating edge of the species' distribution that could be lost if warming trends persist. The loss of the distinct southern genetic heritage could end potential ongoing diversification or speciation processes and impoverishes the adaptive potential of the species as a whole.