The morphology characteristics and the mucous cell distribution in two species of commercial catfish (Pangasius hypophthalmus and Clarias batrachus) were investigated in the present study. To study morphological characteristics, the parameters - such as total length (TL), standard length (SL), body depth (BD), pre-dorsal length (PDL), pre-pectoral length (PPCL), pre-pelvic length (PPVL), pre-anal length (PAL), depth of caudal peduncle (DCP), length of caudal peduncle (LCP), head length (HL), eye diameter (ED), caudal fin length (CFL), pectoral fin length (PFL), and length of dorsal fin base (LAFB) were measured. The mucous cell distributions of the dorsal and ventral parts in the head, abdomen, and GI tract were examined using periodic acid Schiff (PAS) and hematoxylin and eosin (H&E) staining dyes. In P. hypophthalmus, the tail region had the highest mucous cell count, followed by the abdomen and the head, whereas in C. batrachus, the pattern was the opposite. In conclusion, P. hypophthalmus was longer than C. batrachus in most morphological characteristics. The dorsal region had more mucous cells in both species than the ventral region. Overall, C. batrachus was found to have more mucous cell distribution in both ventral and dorsal parts compared to P. hypophthalmus, suggesting that C. batrachus has a better innate immune system than P. hypophthalmus. The sizes of blood cells were also found to be different in both species.