We report for the frst time the presence of flamentous fungi in the water column and sediment in the coastal upwelling ecosystem off central Chile, using molecular tools and epifuorescence microscopy. Positive amplifcations of SSU 18s rDNA with specifc fungal primers were obtained for surface waters and sediments of this coastal ecosystem. Molecular richness obtained from denaturing gradient gel electrophoresis showed a higher number of fungal genotypes in nearshore than offshore sites and in summer than winter. Fungal structures identifed by epifuorescence microscopy in the water column were present as individual flaments or as aggregates of hyphae. We show for the frst time vertical water column profles of fungal biomass in the marine ecosystem. Fungal biomass reached up to 5 µg CL-1 in surface waters during summer and their vertical patterns agreed with those of chlorophyll-a and with the general distribution of microplankton biomass in the ocean. The presence of viable fungi in the coastal ocean encourages us to decipher their role in the processing of marine organic matter and to evalúate their inclusión in the actual paradigm of the microbial loop and in the biogeochemistry of the oceans.