It is proposed that marine fungi are a good alternative for remediation of areas contaminated with antibiotics due to their heterotrophic condition, adaptability to environmental changes, and specific resistance to stressors. With this assumption we investigated the fjords of Southern Chile, which are characterized by salmon farming. We evaluated the concentration of oxytetracycline (OTC) in sediments from different areas surrounding salmon cages. In addition, we isolated fungi species to assess their ability to degrade OTC. Measurable amounts of OTC were detected in deeper sediments located at the eastern sector of cages and rafts (Z= 100 m; 4.62 ± 0.12 to 24.1 ± 1.03 µg g-1). Thirty-eight strains of endemic fungi were isolated and identified in the sediments near the farming center. Among these strains we detected species from the Phylum Ascomycetes, including Penicillium commune, Aspergillus terreus, Beauveria bassiana, Trichoderma harzianum, Epicoccum nigrum and Emericellopsis alkaline. These strains fungi were capable of degrading about 76 to 92% of the OTC present in the culture media. The results of this study constitute a first step into implementing processes that could favor waste bioremediation from marine sediments.