A checklist of the native fishes of the Dhanu River and adjacent waters at Mithamain Upazila under the Kishoreganj district of Bangladesh is prepared with details on their availability, conservation status, habitat preferences, population trends, and threats. Data were collected monthly by field survey, focus group discussions, and personal interviews by using a semi-structured questionnaire and a pictorial check list of fish species. A total of 91 indigenous fish species of 59 genera belonging to 29 families under 11 orders were documented where 17.6%, 27.5%, 31.9%, and 23.1% species were abundantly available, commonly available, moderately available, and rarely available, respectively. Among those, 24 fish species (26.4%) were under the threatened category (3 critically endangered, 11 endangered, and 10 vulnerable) according to the IUCN Bangladesh. Notably, the globally threatened Cirrhinus cirrhosus, Channa orientalis, and Wallago attu were available in the study area. Fish population trends of 24.2% and 59.3% of the entire fish species were found in decreasing trends at the global and national level, respectively. The leading threats to the fish diversity were indiscriminate overfishing followed by fishing by dewatering of wetlands, the katha fishing method, the use of deprecated fishing gears, etc. Minimizing anthropogenic impacts, enacting fishing laws, installing and managing fish sanctuaries, and raising public awareness can be effective for the conservation of existing fisheries resources.