Fungal contamination of shrimp feeds affects the shelf life leading to substantial economic losses. Ultrastructural changes in Penaeus monodon sub-adults fed three different doses (50, 1000 and 2000 ppb) of aflatoxin B1 (AFB1) were studied. At the end of 4 and 8 weeks of experiment, the hepatopancreas of shrimps were observed for ultrastructural changes. The prominent ultrastructural changes in hepatopancreas of the shrimps fed 1000 and 2000 ppb AFB1 were rupture of cell membrane and microvillus border, damage and swelling of mitochondria, fragmentation of endoplasmic reticulum, nuclear vacuolation, chromatin condensation and autophagy. This study helps to decipher the ultrastructural changes and relate the effects on biochemical, pathological, immunological and histological architecture of the shrimps fed AFB1-incorporated feed. The observed ultrastructural changes could serve as indicators in shrimps exposed to toxicants.