Immunohistochemical localization of aromatase, estrogen and estrogen receptor in the digestive tract and enteric neurons of amphioxus is investigated. It was found that immunoreactive proteins of aromatase, estrogen and ER-α and β are expressed in hepatic diverticulum, epithelial cells of anterior and posterior region of midgut, as well as in enteric neurons, while hindgut showed immunonegative. The results suggest that digestive tract of amphioxus may be able to synthesize estrogen and possess endocrine function, like rat gastric epithelium and enteric neurons in mammals. The present study provides authentic morphological evidence for explaining the action mechanism of estrogen in regulating the digestive function of gut and the functional evolution of estrogen, which has important theoretical significance in amphioxus.