Ammonia is one of the most common and pervasive pollutants in the aquatic habitat affecting the health of aquatic animals. It affects the number and morphology of mucus producing cells, resulting in excessive and irregular secretion and alterations in quantity of mucus, which can lead to complications in fish health. A toxicity test on the mucus cells localized on the gills (primary lamellae) and inner operculum epithelial lining of zebrafish Danio rerio at different periods of exposure (24, 48 and 72 h) followed by recovery periods was studied using histopathology, scanning electron microscopy and anterior gradient 2 homologue (agr2) gene expression techniques. Fish samples subjected to low, medium and high external toxic ammonia concentrations (L: 17.21 mg/l, M: 25.81 mg/l and H: 38.91 mg/l NH3-N) were observed to display a higher mucus layer production and active secretion compared with the control. Gill cellular alterations were more severe at 48 and 72 h. A high expression of agr2 was detected at 48 h (L and M) recovery periods and a (H) exposure and recovery period indicating an increase in quantity in newly proliferated alcian blue stained mucus cells and excessive secretion observed by histopathology. Such expression decreased at 72 h resulting in a decrease in mucus cell density and secretion.