Marine microorganisms play a crucial role in ecological balance, biogeochemical cycles and food webs. These microorganisms have developed diverse strategies to adapt to challenging conditions, making them a valuable source for new biotechnological products such as pigments, enzymes and bioactive compounds. Despite the ubiquitous presence of fungi in marine environments, research has mainly focused on bacteria. Thus, the study of marine fungi is still a poorly explored area with great potential for discovering innovative biotechnological tools. The present work focused on the isolation and characterization of filamentous fungi from sediment samples collected in Basque estuaries. Their phenotypic characterization led to the identification of strains potentially able to grow on minimal culture medium supplemented with recalcitrant algal polysaccharides or to produce secondary metabolites. Two isolates were selected for genome sequencing and analysis: 1) Albophoma yamanashiensis for its apparent ability to grow in minimal culture medium supplemented with commercial fucoidan and 2) Marquandomyces marquandii due to its ability to stain the culture medium in yellow, indicative of secretion of pigments and secondary metabolites. Co-culture experiments suggested an inhibitory effect on fungal growth for this secreted fraction, while RNA-seq experiments informed of the set of secondary metabolite gene clusters deregulated under culture conditions inducing pigment secretion. Furthermore, transcriptomic and proteomic experiments on A. yamanashiensis samples suggested that, compared to bacteria, fungi use different enzymatic mechanisms to respond to the presence of fucoidan. Overall, results suggest that the isolates of our library could serve as a source of new enzymatic activities and secondary metabolites.