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 to 7.315±0.570 log cfu g-1 in winter and 6.907±1.114 to 8.044±0.563 log cfu g-1  in summer, whereas tilapia (lean fish) ranged from 5.281±0.690 to 6.251± 0.435 log cfu g-1  in winter and 6.025±0.560 to 7.929±0.562 log cfu g-1  in 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, a number of suggestions can be maintained for the quality of products, including temperature control starting from harvesting by fishermen till handling and consumed by the customers, chilling fish following market conditions, providing safety equipment, and training market workers.