To obtain well spread chromosomes, the cytogenetic protocol for Pangasianodon hypophthalmus and Clarias gariepinus were optimized. This includes, the colchicine concentration (0.01, 0.025, 0.05 %) / exposure duration (1, 3, and 5 h), hypotonic solution (distilled water or 0.075M KCl solution) /exposure duration (30min, 1h, and 2h), the time of cell suspension preparation (at hypotonic treatment or before slide preparation) and chromosome aging period (0, 3, and 7 days in Carnoy's fixative). In addition, the type (i.e. fin, gill or kidney) and the amount of tissue (10, 50, 100 or 150mg) were also investigated. Regardless of the species, the result obtained showed that well-spread chromosomes could be obtained using the following optimized protocol: Juveniles are injected with 0.05% colchicine (at 1mlkg-1) and allowed to swim for 3h. Then, 50mg of gill tissue is made into cell suspension in 0.075M KCl for 1h. The cell suspension is treated in Carnoy's fixative (changed 3times at 20min interval) and then aged for three days. Finally, chromosome slides are made and stained with 10% Giemsa for 1h.