This document summarizes a study on the histological decay of the stomach in milkfish (Chanos chanos) reared in a traditional brackishwater pond in East Java, Indonesia. Several factors were found to contribute to deterioration of the stomach, including environmental stress from heavy metals in the water, high ammonia levels, a shift in the natural food composition to cyanobacteria, and infection by the Myxobolus parasite. Earlier harvest, higher mortality, and smaller fish size compared to normal indicated declining productivity of traditional milkfish aquaculture in the region in recent decades.