This study was conducted to determine and compare the organoleptic quality and the bacterial load of lean fish (Oreochromis niloticus) and fatty fish (Pangasianodon hypophthalmus). Empirical data were collected from four fish markets in Northeast Bangladesh (Sylhet and Sunamganj) considering two seasons. The Total Viable Count (TVC) of fatty fish (pangus) ranged from 6.213±0.633 log cfu g-1 to 7.315±0.570 log cfu g-1 in the winter and 6.907±1.114 log cfu g-1 to 8.044±0.563 log cfu g-1 in the summer, whereas tilapia (lean fish) ranged from 5.281±0.690 log cfu g-1 to 6.251± 0.435 log cfu g-1 in the winter and 6.025±0.560 log cfu g-1 to 7.929±0.562 log cfu g-1 in the summer. The sanitary conditions and fish storage facilities in the region were found to be poor and didn’t comply with ICMSF standards. In summary, there are a number of suggestions that can be maintained for the quality of products, including controlling the temperature from fishermen to customers, chilling fish following market conditions, providing safety equipment, and training market workers.