<p>The microbiome plays a crucial role in host health, a recognition that has grown in recent years across many organisms. These host–microbiome associations may not be uniform at the host-species level; instead, they could differ among geographically separated populations, potentially reflecting adaptation to local conditions. In the Cantabrian Sea, rising seawater temperatures are shifting the distribution of many macroalgae species. Among them, <i>Gelidium corneum</i>, a key habitat-forming red alga, is showing a reduction in biomass, yet remains present in this coastal region. Given the wide geographic separation of its populations, it is plausible that <i>G. corneum</i> harbours distinct diatom-dominated microbial communities signalling local adaptation. In this study, we characterized the epibiotic diatom communities associated with <i>G. corneum</i> across three populations spanning 340&#xa0;km along the northern Iberian Peninsula. Sampling was conducted at two depths, 5 and 12&#xa0;m, in autumn 2022 and spring 2023. Using an integrated morphological and molecular approach, we identified 268 diatom taxa across 94 genera. Our results revealed a marked seasonal effect on community composition, and all environmental variables, except irradiance, significantly shaped diatom distribution. Certain taxa were consistently associated with seasons and specific locations, indicating site-specific associations. Taken together, these findings show that <i>G. corneum</i> supports a highly diverse and dynamic epibiotic diatom community. As the first study to examine these associations in this species, our results suggest that environmental factors are the main drivers of diatom community variation. However, favourable spring conditions may enhance differentiation among <i>G. corneum</i> populations, allowing the development of more distinct microbial assemblages that may include dominant taxa providing potential mutual benefits.</p> Graphical Abstract <p></p>