Considered as holobiont systems, marine macroalgae and their microbiota constitute functional units displaying a large diversity of interactions. Main factors driving the assembly of epiphytic microbiota, and subsequent interactions with the host, are often associated to environmental differences but also to host taxonomy displaying specific chemical properties. Here, through a large sampling effort focused on the brown algal genus Taonia (Dictyotales) on both the French Mediterranean and Atlantic coasts, we aimed to highlight the relative importance of the effects of environment, host taxonomy and surface metabolome on the epibacterial community of these seaweeds. Phylogenetic analyses revealed two distinct clusters, one grouping only the specimens from the French Mediterranean coasts and the second one composed of samples from Brittany. Both metabarcoding and surface metabolomics revealed clear differences between Mediterranean thalli and those collected in Brittany. Strong environmental differences associated with algae from these two different geographical areas could both be involved in this clustering. For example, oxidative stress due to higher irradiance intensities might induce a higher expression of fucoxanthin in Mediterranean samples, while higher eutrophication levels could explain the higher abundance of Alteromonas spp. on algal samples from Brittany coast. In a lesser extent, genetic differences observed between thalli from these two locations could also influence surface metabolomes and thus host-microbiota interactions.