North Eastern region of Bangladesh is very promising for freshwater capture fisheries, nevertheless comprehensive assessment on faunal composition and diversity asseblages of natural wetlands are scant.This study identifies the occurrence, different biodiversity indices and composition of fish with various gear types by means of qualitative and quantitative approaches in Tanguar haor and Dekar haor. A total of 75 fish species were identified, of which 53% were Cypriniformes, followed by Siluriformes (15%), Perciformes (14%), Channiformes (7%) and Clupeiformes (4%). Among the identified taxa 42 species were not threatened, 12 vulnerable, 11 endangered and 8 critically endangered. The values of diversity indices explicitly Shannon-Weiner (H’), Pielou eveness (J’), Margalef richness (d) and Simpson dominance (c) indices indicated that Tanguar haor were more diversified and evenly distributed than Dekhar haor. For effective management of the haors comprehensive stock assessment, establishment of fish sanctuaries, and combination of input and output control is suggested.