The marine ecosystem is an extraordinary reserve of pharmaceutically important, bioactive compounds even in this “synthetic age”. Marine algae-associated endophytic fungi have gained prominence as an important source of bioactive compounds. This study was conducted on secondary metabolites of Chaetomium globosum-associated with marine green alga Chaetomorpha media from the Konkan coastline, India. Its ethyl acetate extract (CGEE) exhibited an IC50 value of 7.9 ± 0.1 µg/mL on MCF-7 cells. CGEE exhibited G2M phase cell cycle arrest, ROS production and MMP loss in MCF-7 cells. The myco-components in CGEE contributing to the cytotoxicity were found by Gas Chromatography/Mass Spectrometry analyses. Chrysin, a dihydroxyflavone was one of the forty-six myco-components which is commonly found in honey, propolis and passionflower extracts. The compound was isolated and characterized as fungal chrysin using HPLC, UV–Vis spectroscopy, LC–MS, IR and NMR analyses by comparing with standard chrysin. The purified compound exhibited an IC50 value of 49.0 ± 0.6 µM while that of standard chrysin was 48.5 ± 1.6 µM in MCF-7 cells. It induced apoptosis, G1 phase cell cycle arrest, MMP loss, and ROS production. This is the first report of chrysin from an alternative source with opportunities for yield enhancement.