Present study concerned with exposure of herbicide, almix in stomach and intestine of Heteropneustes fossilis at a dose of 8 g/acre and 66.67 mg/l for 30 days under field and laboratory conditions respectively on histopathological and ultrastructural levels. Stomach showed vacuolation in gastric glands, thinning of mucosal folds and disappearance of the brush border under laboratory condition, but secretion of mucus from damaged columnar epithelial cells (CEC) were prominent in field. In stomach, scanning electron microscopy (SEM) showed fragmentation of CEC and damage in microridges, while transmission electron microscopy (TEM) displayed deformed mitochondria, vacuolation and damage in tubular network under laboratory condition but in field condition alterations in shape of CEC and mucin droplets under SEM, and cellular vacuolation under TEM study were prominent. In intestine, disruption and vacuolation of connective tissue of lamina propria and severe damage in CEC were seen under laboratory condition but in field condition liver showed almost normal appearance. Under SEM observation intestinal epithelium showed shrinkage in mucosal folds, empty mucus pit and secondary cellular growth in laboratory condition but debris of fragmented secondary mucosal folds were prominent under field condition. On the other hand, TEM study showed dilated mitochondria and swelled endoplasmic reticulum under laboratory condition but intestinal epithelial cells remain unaltered under field condition. Therefore, present study revealed that the responses were more profound in laboratory condition than field condition. Finally, these responses could be considered as biomarker of herbicide toxicity in aquatic ecosystem for monitoring the state of the entire ecosystem.