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Endophytic fungi can thrive without producing illness or injury to the host plant tissues, and they are also one of the major natural sources of bioactive compounds. The objective of the present study was to assess the anticancer potential of fungal extracts obtained from Ceriops decandra and in-silico-based identification of the anticancer constituents from those fungal extracts. Endophytic fungi were isolated and identified by internal transcribed spacer (ITS-rDNA) sequence analysis. The fungal crude extract was subjected to column chromatography and different fractions were screened for bioactive compounds using Gas Chromatography Mass Spectroscopy (GCMS). Fusarium oxysporum, Chlonostachys sp., Fusarium solani were identified from C. decandra. Eighty (80) compounds were identified from these endophytic fungi through GCMS analysis. A molecular docking study of the identified compounds confirmed the anti-cancer potential of breast cancer cells through the estrogen receptor, with good binding affinities (−9.17 to −7.19 kcal/mol) and interaction patterns. Furthermore, in molecular dynamic simulation studies, Isoparvifuran (CID_617473) and 2,4-di-tert-butylphenol (CID_7311) revealed a stable complex with the target protein of estrogen receptor alpha. The result of the study showed that C. decandra harbors diverse group of endophytic fungi that can be a potential source of bioactive (Isoparvifuran and 2,4-di-tert-butylphenol) pharmaceuticals to treat breast cancer through modulation of estrogen receptor alpha.