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A comparative study of benthic fauna between Rajdhala beel and Padmai beel of Netrakona District under different management system was carried out from July 1999 to January 20OO. An average number of 1113 and 1175 organisms/m2 were obtained from Rajdhala heel and Padmai beel respectively. A total of 22 taxa belonging to 8 diverse groups, Oligochaetes, Chironomids, Molluscs, Ceratopogonids, Diptera (other than Chironomids and Ceratopogonids), Ephemeroptera, Leeches and Crustaceans were recorded. Oligochaetes were dominated and constituted 46% and 49% ofthe total benthic population in Rajdhala heel and Padmai beel respectively. The next dominant group was the Chironomids, which constituted 31% and 30% of the total benthic population in Rajdhala beel and Padmai beel respectively. The highest number 1279 and 1437 individuals/m2 of benthic fauna was recorded in December from Rajdhla beel and Padmai bee! in respectively. The lowest number of benthic fauna 869 and 914 individuals/m2 were found during September and July from Rajdhala beel and Padmai beel respectively. Monthly variation of benthic fauna among two beels were found statistically significant (p<0.05). The numerical distributions of benthic fauna was found to be varied with depth ranges. However, the depth wise variation of total benthic fauna between two heels was not found statistically significant. Fish yield of Rajdhala beel (488 kg/ha/yr) was appreciably higher than the Padmai beel (250 kg/ha/yr).