The effect of Endotaf (Endosulfan, 35%) pesticide was studied on nitrogen fixation efficiency of Cylindrospermum musicola, Calothrix javanica and Westiellopsis prolifica at different concentrations of pesticide in the nitrogen free BG-11 medium. Total nitrogen fixed by blue-green algal species was estimated by conventional Micro- kjeldahl method in the laboratory cultures at each concentration of Endotaf pesticide. The results obtained during the present investigation indicated a progressive decrease in the total nitrogen content of the tested blue-green algae with increasing concentrations of the Endotaf pesticide. However, nitrogen fixation of most of the blue-green algae was also increased at the lower doses of pesticide. The consequences of the results revealed that Calothrix javanica was emerged as most compatible and tolerant to the increasing Endotaf pesticide doses than the other tested blue-green algal species. On the other hand, Cylindrospermum musicola was found to be highly susceptible as even at 2.5 ppm of Endotaf. Calothrix species was capable to tolerate upto 10 ppm of Endotaf while in Westiellopsis prolifica and Cylindrospermum musicola, the pesticide tolerance range was found to be upto 5 ppm and 2.5 ppm with Endotaf, respectively. Further increase in pesticides concentrations a gradual decline in the total nitrogen content occurred in all the tested blue-green algal strains. It is concluded that indiscriminate use of these pesticides may cause adverse effects on the nitrogen fixing blue-green algae of various crop fields, which has a direct influence on total productivity. Since it is essential to screen efficient blue-green algal strains those are capable of growing and fixing nitrogen at higher rate even in presence of recommended doses of the agrochemicals including pesticides, before their inoculation into the field.