Global change is imposing significant losses in the functional traits of marine organisms. Although areas of climatic refugia ameliorate local conditions and help them to persist, the extent to which mesoscale effects contribute for intraregional variability on population traits and conservation is uncertain. Here we assess patterns of conservation status of Fucus guiryi, the main intertidal habitat-forming seaweed in the Strait of Gibraltar (southern Spain and northern Morocco). We investigated the demography, reproductive phenology, and morphology at northern and southern side populations. Population traits were compared seasonally within populations from each side, and at spatial scale in early summer 2019. In the last decade three populations became extinct; two marginal populations had dispersed individuals with a narrower fertility season and miniaturized individuals below 3 cm; and five populations showed variable density and cover with more than 20% of reproductive individuals over the seasons. Highest density, cover, morphology, and reproductive potential was detected at one population from each side, suggesting local-scale climatic refugia in upwelling areas located inside marine protected areas. Southern recruits were more warm-tolerant but grew less at colder conditions than northern ones, revealing a mesoscale heterogeneity in thermal affinities. This study evidenced functional losses and distinct reproductive strategies experienced by F. guiryi at peripheral locations and urges to prioritize its conservation and restoration at contemporary climatic refugia.