Two new spiroketal derivatives with an unprecedented amino group, 2'-aminodechloromaldoxin (1) and 2'-aminodechlorogeodoxin (2), along with one known analogue dechloromaldoxin (3), were isolated from the plant endophytic fungus Pestalotiopsis flavidula. Their structures were elucidated on the basis of extensive spectroscopic analysis. The purification was cytotoxicity-guided which indicated the extract, fractions and compounds were evaluated in vitro for anti-proliferative activity against a panel of human cancer cell lines. The results showed compounds 1 and 2 with moderate cytotoxicity while 3 was inactive, which suggested -NH2 group might play a very important role for their cytotoxicity. This is the first study for P. flavidula and the first time to report the spiroketal derivatives as alkaloids from the Pestalotiopsis genus.