Secondary metabolites of Clitocybe nuda displayed antimicrobial activity against Phytophthora capsici. The culture filtrate of C. nuda was extracted with ethanol and chromatographically separated on a Sephadex LH-20 column and fractionated on a silica gel column to give eight fractions. These fractions were tested for the ability to inhibit zoospore germination of P. capsici . The most active fraction was further purified by silica gel column chromatography to yield three compounds: 2-methoxy-5-methyl-6-methoxymethyl-p-benzoquinone (1), 6-hydroxy-2H-pyran-3-carbaldehyde (2), and indole-3-carbaldehyde (3), all new to C. nuda. At a concentration of 500 mg/L, compound 3 showed complete inhibition of zoospore germination, while compounds 1 and 2 showed inhibition rates of 97 and 86%, respectively. To our knowledge, compound 1 is a newly discovered compound and, for the other two compounds, this is the first report in C. nuda. These compounds are potential candidates for new edible fungi-derived pesticides for the control of plant diseases.