Many fungi produce pentaketide-derived melanin (a polymer of 1,8-dihydroxynaphthalene, 1,8-DHN), which is essential for appressorium melanization and host penetration by pathogens like Colletotrichum lagenarium. The melanin biosynthesis pathway begins with the formation of 1,3,6,8-tetrahydroxynaphthalene (1,3,6,8-THN) from malonyl-CoA via a polyketide synthase (PKS1). While reductase and dehydratase inhibitors have been used to control fungal diseases, no specific PKS1 inhibitor was available. An in vitro PKS1 reaction system (using C. lagenarium PKS1 expressed in Aspergillus oryzae) was developed for inhibitor screening. Screening microbial metabolites revealed Streptomyces sp. No. 4a produces PKS1 inhibitors; abikoviromycin (1) and dihydroabikoviromycin (2) were isolated from its culture filtrate as active principles. This paper describes the isolation and biological activity of 1 and 2 as PKS1 inhibitors. PKS1 inhibitory assays showed 1 (IC50 5 μg/ml) was more potent than 2 (IC50 30 μg/ml). MIC values of 1 and 2 against C. lagenarium were much higher than their IC50 values. In an in vivo melanin induction system, 1 dose-dependently inhibited C. lagenarium melanin production without affecting fungal growth. These results demonstrate for the first time that PKS1 inhibitors are candidates for selective inhibition of melanin production in pathogenic fungi.