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The brown algal genus <i>Fucus</i> provides essential ecosystem services crucial for marine environments. Macroalgae (seaweeds) release dissolved organic matter, hence, are under strong settlement pressure from micro- and macrofoulers. Seaweeds are able to control surface epibionts directly by releasing antimicrobial compounds onto their surfaces, and indirectly by recruiting beneficial microorganisms that produce antimicrobial/antifouling metabolites. In the Kiel Fjord, in the German Baltic Sea, three distinct <i>Fucus</i> species coexist: <i>F. vesiculosus</i>, <i>F. serratus</i>, and <i>F. distichus</i> subsp. <i>evanescens</i>. Despite sharing the same habitat, they show varying fouling levels; <i>F. distichus</i> subsp. <i>evanescens</i> is the least fouled, while <i>F. vesiculosus</i> is the most fouled. The present study explored the surface metabolomes and epiphytic microbiota of these three <i>Fucus</i> spp., aiming to uncover the factors that contribute to the differences in the fouling intensity on their surfaces. Towards this aim, algal surface metabolomes were analyzed using comparative untargeted LC-MS/MS-based metabolomics, to identify the marker metabolites influencing surface fouling. Their epiphytic microbial communities were also comparatively characterized using high-throughput amplicon sequencing, to pinpoint the differences in the surface microbiomes of the algae. Our results show that the surface of the least fouling species, <i>F. distichus</i> subsp. <i>evanescens</i>, is enriched with bioactive compounds, such as betaine lipids MGTA, 4-pyridoxic acid, and ulvaline, which are absent from the other species. Additionally, it exhibits a high abundance of the fungal genera <i>Mucor</i> and <i>Alternaria</i>, along with the bacterial genus <i>Yoonia-Loktanella</i>. These taxa are known for producing antimicrobial/antifouling compounds, suggesting their potential role in the observed fouling resistance on the surface of the <i>F. distichus</i> subsp. <i>evanescens</i> compared to <i>F. serratus</i> and <i>F. vesiculosus</i>. These findings provide valuable clues on the differential surface fouling intensity of <i>Fucus</i> spp., and their importance in marine chemical defense and fouling dynamics.