Aspernigerin (1), a novel cytotoxic alkaloid consisting of an unprecedented structural framework has been isolated from the extract of a culture of Aspergillus niger IFB-E003, an endophyte in Cyndon dactylon. Its structure was elucidated on the basis of comprehensive NMR spectral analysis and confirmed by single-crystal X-ray analysis. Aspernigerin (1) has been shown to be cytotoxic to the tumor cell lines nasopharynyeal epidermoid KB, cervical carcinoma Hela, and colorectal carcinoma SW1116 with corresponding IC(50) values of 22, 46, and 35 microM, respectively. A feasible total synthetic route for aspernigerin (1) has been established for further pharmacological research.