The fungicidal activities of Coptis japonica (Makino) extracts and their active principles were determined against Botrytis cineria, Erysiphe graminis, Phytophthora infestans, Puccinia recondita, Pyricularia grisea, and Rhizoctonia solani using a whole plant method in vivo, and compared with natural fungicides. The responses varied according to the plant pathogen tested. At 2,000 mg/l, the chloroform and butanol fractions obtained from methanolic extracts of C. japonica exhibited strong/moderate fungicidal activities against B. cinerea, E. graminis, P. recondita, and Py. grisea. Two active constituents from the chloroform fractions and one active constituent from the butanol fractions were characterized as isoquinoline alkaloids, berberine chloride, palmatine iodide, and coptisine chloride, respectively, using spectral analysis. Berberine chloride had an apparent $LC_{50}$ value of approximately 190, 80, and 50 mg/l against B. cinerea, E. graminis, and P. recondita, respectively; coptisine chloride had an $LC_{50}$ value of 210,20, 180, and 290 mg/l against B. cinerea, E. graminis, P. recondita, and Py. grisea, respectively; and palmatine iodide had an $LC_{50}$ value of 160 mg/l against Py. grisea. The isoquinoline alkaloids were also found to be more potent than the natural fungicides, curcumin and emodin. Therefore, these compounds isolated from C. japonica may be useful leads for the development of new types of natural fungicides for controlling B. cinerea, E. graminis, P. recondita, and Py. grisea in crops.