In the present study experiments were conducted to evaluate the toxic effects of azadirachtin in ciliated models Paramecium caudatum and Oxytricha fallax, which are considered as ideal organisms for investigating water quality fluctuations and risk assessment. Cell viability, cell morphology, cytopathological responses and macronucleus tests were performed using Paramecium caudatum and Oxytricha fallax to different concentrations of azadirachtin. The calculated LC50 value of azadirachtin against mortality curve for 3hrs exposure was found 239.44±13.94 and 263.006±13.1ppm to Paramecium caudatum and Oxytricha fallax respectively. Paramecia were more sensitive than Oxytricha to azadirachtin. Azadirachtin affected cell bahaviour, locomotion and cellular morphology of both the organisms. After a short period of exposure (20min to 30 min), there was an increase in the number of necrotic cells with typical features like blackening of cytoplasm, blebbing, macronuclear changes and leaking of internal contents leading to cell lysis. Morphological changes occured in the shape of macronucleus which were dependent on concentration. The macronuclear changes were significant showing deformities such as rod shape, marginalization of nucleus, fragmentation, uneven division and total diffusion of nucleus. The present findings indicate a possible necrotic and genotoxic effect of azadirachtin on both the organisms and these assays suggest the potential of ciliates for ecotoxicological studies.