Adult African catfish (Clarias gariepinus) were used to investigate the effects of prespawning prophylactic disinfection during a seven days quarantine period on the breeding performance and the possible histopathological influences on C. gariepinus brooders. Based on broodfish sex; a total of 36 females were stocked into 6 tanks (6 females tank-1) and 18 males were stoked into other 6 tanks (3 males/tank) signifying three treated groups (T1: T3) of two replicates (6 females+3 males/replicate). T1 was assigned as a control non-treated broodfish, whereas T2 broodfish was disinfected with formalin (FA) (15 ppm) for 6 h and T3 broodfish were disinfected with malachite green (MG) (1 ppm) for 45 minutes. Brooders treated with MG (T3) delivered lower egg numbers, lower hatching percent and high percentage of larval deformity. Additionally, pronounced histopathological lesions were observed in the liver, testis and ovaries of both the FA and MG-treated catfish that is to give a further explanation for the declined breeding performance of both groups. Herein, the pre-spawning disinfection of C. gariepinus during the quarantine period is not necessary especially when proper management, transportation and handling is to be followed. Nevertheless, if prespawning disinfection to be applied; the MG should not be prescribed for C. gariepinus broodfish unless no other cheap and much safer disinfectants rather than FA existed. But still, a future research is required to explore its possible negative effects on both reproductive efficiency and the prospected histopathological changes of broodfish being recovered from FA application.