A new anthraquinone derivative, lupinacidin C (1), was isolated from the endophytic actinomycete Micromonospora lupini. The structure was elucidated on the basis of spectroscopic analyses, and the absolute configuration was determined by total synthesis. Lupinacidin C (1) exhibited the most potent inhibitory effects among the congeners on the invasion of murine colon carcinoma cells into the reconstituted basement membrane.