Nonylphenols (NPs) are known as Endocrine Disputing Chemicals (ECDs) and Persistent Organic Pollutants (POPs) and have attracted continuous attention. Biodegradation is one of the effective ways for pollutant removal in aquatic, sedimentary and soil environments. In this study, two estuarine derived fungi strains, NPF2 and NPF3, were screened from Moshui river estuarine sediment and identified as genus Aspergillus. The growth curves of the two strains as well as the removal and degradation rates for 4-n-NP in Potato Dextrose(PD)medium were used to evaluate their degradation ability. Both strains showed high efficiency for 4-n-NP degradation with 86.03% and 98.76% removal rates in 3 days for NPF2 and NPF3, respectively. Determination of degradation intermediates by LC MS suggested that the mechanisms for 4-n-NP biodegradation by NPF2 and NPF3 are quite different. Some key functional genes for the two strains also provided supplementary evidences for the different biodegradation mechanism. On strain NPF2, with participation of Coxl, 2 and 3, 4-n-NP degradation starts from reaction at the terminal of the long alkyl chain. The chain reduces one carbon atom once within a cycle of hydroxylation, subsequent oxidation at alpha-C position and decarboxylation. However, on NPF3, with involvement of sMO, Cel7A, Ce17B and ATEG-00639, 4-n-NP degradation starts from benzene ring, converting into fatty acids. The latter bio-pathway was the first time reported for NPs degradation on fungi.