Alkylphenols (APs)—nonylphenol (NP) and octylphenol (OP)—are well-known environmental contaminants due to their widespread application and have been identified as endocrine-disrupting chemicals. A novel APs-tolerant fungus designated F6 was isolated from the bottom sediments of the coastal part of the Eastern Gulf of Finland (Neva Bay) and was identified as Aspergillus tubingensis F6 based on ITS sequencing and morphological analysis. The APs presence caused morphological and ultrastructural changes in fungal cells. Major differences were detected in mitochondria, vacuoles, and cell walls. Nonenzymatic antioxidants—pigments, reduced glutathione, exopolysaccharides—played important roles in A. tubingensis F6 resistance to APs toxicity. A low level of lipid peroxidation showed that the protective effects of the antioxidant system were sufficient despite the fact that antioxidant enzymes activity levels were low. Another defense response employed by A. tubingensis F6 against the tNP- and 4-tert-OP-induced stress was based on the ability of the strain to efficiently utilize xenobiotics. After 120 h of cultivation, < 10% of APs (initially added to the culture at 100 mg/l) remained in the culture medium of A. tubingensis F6. The APs degradation by A. tubingensis F6 led to the formation of nontoxic products. These data indicate the potential role for A. tubingensis F6 in APs degradation in natural environments, as well as its possible biotechnological application in wastewater treatment to remove xenobiotics with endocrine activity. To our knowledge, this is the first report demonstrating that marine-derived fungus A. tubingensis strain is capable of utilizing branched-chain NP and OP.