Carboline alkaloids are a class of important heterocyclic natural products, which usually present extensive bioactivities. During the course of our research for active compounds from natural products, the pityriacitrin and pityriacitrin B belonged carboline alkaloids have been isolated from a Chinese Burkholderia sp. NBF227, which indicated potential antifungal activities. So, in order to develop these carboline alkaloids as potential fungicidal agents, a series of pityriacitrin derivatives were investigated for their antifungal activities against Phytophthora capsici, Sclerotinia sclerotiorum, Botrytis cinerea and Rhizoctonia solani, and the results demonstrated that compounds 4, 10 and 19 displayed broad-spectrum antifungal activities. In addition, in vivo bioassay also indicated that compounds 4 and 10 could protect the pepper leaves and grape fruits against infection by P. capsici and B. cinerea, respectively. The possible mechanism of antifungal action for these compounds was also explored.