Aquaculture products (fish) can harbor pathogenic bacteria which are part of the natural micro-flora of the environment. The current study was carried out for the extraction and identification of fish pathogenic microbes from Baime fish (Mystus armatus). Diseased fresh-water fishes were collected from different water bodies and fish landing centers of two study areas, namely the City area, Jhenaidah region. Bacteria are one of the important causative agents of fish diseases in both wild and cultured fish and are responsible for serious economic losses. Pathogenic bacteria strain was isolated from the infected area of Baime (M. armatus) fish skin. After isolation, isolates were finally identified by their desired morphological, characteristics, and biochemical test. They were gram-negative, rod-shaped bacteria that showed positive reaction for catalase, able to ferment glucose and one is citrate negative and another is citrate positive. After being persuaded above-mentioned test isolates were identified as genus Aeromonas and Pseudomonas. The ulcer type disease of M. armatus, the isolate was tested against several antibiotics’ treatment. Pseudomonas strains isolated from M. armatus is susceptible to penicillin G (10 μg), amoxicillin (10 μg), erythromycin (15 μg), Tetracycline (30 μg), Kanamycin (30 μg), moderately susceptible to Co-trimoxazole (25 μg), and Resistance to ceftazidime (10 μg). Aeromonas strains isolated from M. armatus is susceptible to amoxicillin (10 μg), erythromycin (15 μg), Tetracycline (30 μg), moderately susceptible to ceftazidime (10 μg), and Resistance to Co-trimoxazole (25 μg), penicillin G (10 μg), Kanamycin (30 μg). The results of the present study constitute an advance in the available diagnostic and bacterial pathogens in fish farms.