A new phthalazinone derivative, named amycophthalazinone A (1), and a new isoflavonoid glycoside, 7-Omethyl- 5-O-α-L-rhamnopyranosylgenestein (2), along with an isoflavonoid glycoside, 7-O-α-D-arabinofuranosyl daidzein (3) firstly found from natural sources, and eight known compounds (4–11), were isolated from the culture broth of the lichen-associated Amycolatopsis sp. YIM 130642. The structures of new compounds were elucidated on the basis of spectroscopic analysis. Compound 1 was the first example of naturally occurring phthalazinone derivative. The antimicrobial activities of all compounds towards five pathogenic strains were evaluated by a broth microdilution assay. Compound 1 exhibited the most potent inhibitory activity against Staphylococcus aureus, Salmonella typhi, and Candida albicans with MIC values of 32, 32, and 64 μg/mL, respectively. Keywords: Amycolatopsis; Lichen; Phthalazinone; Isoflavonoid; Antimicrobial activity.