Bacterial pathogens are the causative agents of the most serious infectious disease in cultured fish causing mortalities and severe economic losses. This study evaluates molecular characterization and pathogenic effects of Alcaligenes faecalis isolated from hatchery-reared Clarias gariepinus juveniles. The bacterial isolates were characterized using biochemical tests, morphological traits, and 16S rRNA gene. One hundred and twenty Clarias gariepinus juvenile were acclimatized and divided into two groups (infected and control) with three replicates (20 fish per replicate). The fish were infected with A. faecalis isolates at a rate of 8.0 x 108 CFU/ml by immersion. The control group were not infected. The control and infected groups were observed for 14 days, mortalities, clinical signs, skin, and gross lesions were recorded. Haematology and histopathology of both control and infected group of fish were studied. Alcaligenes faecalis isolates showed evolutionary relationship with NCBI-reported isolates from India, Kenya, Pakistan, Italy, China, and Russia. The mortality rate was 0% and 60.0% in control and infected fish, respectively. Anaemia, heteropenia, leukocytopenia, and lymphocytopenia were observed in the infected group. The histopathological changes in the skin, gill and liver sections showed degeneration of surface epithelial cells, loose connective tissues collagen in the dermal layer, fused filament in the gill, and abnormal hepatocytes with severe glycogenic vacuolation on the cytoplasms. Alcaligenes faecalis was pathogenic and caused organ damages in infected African catfish. Proper diagnosis is a necessity for control of bacterial infections in Nigeria aquaculture industry