Present study was designed to evaluate the adverse effect of glyphosate-based herbicide, Excel Mera 71 in Anabas testudineus on comparative basis under field and laboratory conditions. Field (750 g/acre) and laboratory (17.2 mg/L) experiments were performed for a period of 30 days. For field experiment special type of cages were prepared. Fish gill, liver, and kidney were analyzed for histology and ultrastructural responses. A significant increment in morphometric indices (DTC) was observed in gill, liver and kidney of A. testudineus under laboratory condition (p < 0.05) and responses showed the degree of pathogenicity in the order of liver > kidney > gills. However, under field study significant increase in DTC value was observed in gill and liver (p < 0.05). Among the scanning electron microscopic (SEM) observations necrosis and loss of microridges, and damage in stratified epithelial cells were prominent in gill, although higher prevalence of alterations was observed under laboratory study than field study. Additionally, transmission electron microscopic (TEM) observations also depicted higher prevalence of pathological lesions under laboratory study compared with field observation. Among the TEM observations damage in chloride and pavement cells, degenerative mitochondria and nucleus (in gill); severe vacuolation, necrosed nucleus and vesiculated network in case of liver and degenerated epithelial cells, cytoplasmic vacuolation, and damage in proximal convoluted tubules (PCT) in case of kidney were prominent. Therefore, these findings demonstrated that Excel Mera 71 induces significant damage in tissues of A. testudineus and these responses might be considered as biomarkers for monitoring herbicidal toxicity on fish in aquatic body.