Effects of two different doses, treatment I (0.30 ppm) and treatment II (0.15 ppm) of paraquat, were investigated on mRNA transcript of the catalase gene (cat) and CAT activity in zebrafish. We determined tissue-specific distribution of zebrafish cat and bioinformatics analysis. Muscle, liver, intestine, heart, kidney, brain, eye, gills, swim bladder, skin, ovary and testis tissue samples from three female and three male fish were dissected to detect tissue-spesific distrubition while liver and gill tissues were dissected to evaluate the effect of acute stress in zebrafish. The steady-state level of zebrafish cat transcript in gill (311±11.32) was lower than liver (595.53±14.41) but higher than muscle (132.89±9.21), testis (120.03±6.99), kidney (118.96±8.87), ovary (104.31±8.22), intestine (37.28±3.11), brain (19.17±2.01), eye (18.30±2.10), heart (15.79±2.01), spleen (7.7±0.91), swim bladder (6.97±0.21), and skin (4.59±0.31). Expression of cat was significantly decreased in liver and gill tissues after exposure to two concentrations of paraquat (p<0.05). Measurement of enzyme activities in zebrafish, exposed to 0.30 and 0.15 ppm of paraquat for 72 h duration, showed significant (p<0.05) variations in CAT activity compared to that of the control. Different steady-state levels among tissues in zebrafish could be explained by duplicated genes in teleost fish that arose through teleost specific-whole genome duplication exhibiting a dissimilar tissue distribution.