Six new alkaloids including four new chromeno[3,2-c]pyridines, diaporphasines A-D (1-4), and two new isoindolinones, meyeroguillines C and D (6-7), as well as three known compounds meyeroguilline A (5), 5-deoxybostrycoidin (8), and fusaristatin A (9), were isolated from an endophytic fungus Diaporthe phaseolorum SKS019. Their structures were determined by analysis of 1D and 2D NMR and mass spectroscopic data. Compounds 1-9 are alkaloid components reported for the first time from the Diaporthe sp., and diaporphasines A-D (1-4) are the third examples of alkaloids possessing the unique chromeno[3,2-c]pyridine nucleus. All isolated compounds 1-9 were evaluated for their cytotoxic activity in vitro using MDA-MB-435, HepG2, MCF10A, HCT116, and NCI-H460 human cell lines. Compound 8 exhibited cytotoxicity against MDA-MB-435 and NCI-H460 human cancer cell lines with IC50 values of 5.32 and 6.57μM, respectively, and compound 9 showed growth-inhibitory activity against MDA-MB-435 human cancer cell line with IC50 value of 8.15μM.