An anion exchange chromatographic column (DEAE-650C) and a cation exchange chromatographic column (CM-650C) were connected in series on a perfusion chromatography workstation. The crude extract of bitter melon seeds flowed through the two columns and the unadsorbed fraction on the DEAE-650C column was then directly readsorbed on the CM-650C column. Two protein components with antifungal activity were eluted from the cation exchange chromatographic column by linear salt gradient. Both of them were found to be homogeneous by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and their relative molecular masses were estimated to be about 30 000. Their N-terminal amino acid sequences are DVSFRLSGADPRSYGMFI and DVNFDLSTATAK. All of the above suggested that they are alpha-momorcharin (alpha-MMC) and beta-momorcharin (beta-MMC), respectively, two type I ribosome-inactivating proteins (Rips) of bitter melon seeds. a-MMC shows antifungal activity against Fusarium oxysporum and Pythium aphanidermatum, while beta-MMC shows antifungal activity against Pythium aphanidermatum. But they are not against Sclerotium rolfsii. In the study, quantitative recoveries of alpha-MMC and beta-MMC were 13.8% and 8.0%, respectively, from decorticated seeds by ion exchange chromatographic columns in series.