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Coccidiosis, caused by apicomplexan parasites of the genus Eimeria , inflicts severe economic losses to the poultry industry around the globe. In the present study, ITS-1 based species specific nested PCR revealed prevalence of E . acervulina , E . brunetti , E . maxima , E . mitis , E . praecox , E . necatrix and E . tenella in 79.2%, 12.5%, 64.6%, 89.6%, 60.4%, 64.6% and 97.9% poultry farms of north India, respectively. The ITS-1 sequences of different Eimeria spp. from north India were generated and analyzed to establish their phylogenetic relationship. The sequence identity with available sequences ranged from 80 to 100% in E . tenella , 95 to 100% in E . acervulina , 64 to 97% in E . necatrix , 96 to 99% in E . brunetti and 97 to 98% in E . mitis . Only long ITS-1 sequences of E . maxima could be generated in the present study and it had 80–100% identity with published sequences. Two out of the four ITS-1 sequences of E . maxima had mismatches in the published nested primer sequences from Australia, while one sequence of E . necatrix had a mismatch near 3′ end of both forward and reverse published nested primer sequences, warranting for the need of designing new set of degenerate primers for these two species of Eimeria . In the phylogenetic tree, all isolates of E . acervulina , E . brunetti , E . mitis , E . tenella and E . necatrix clustered in separate clades with high bootstrap value. E . maxima sequences of north Indian isolates grouped in a long form of E . maxima clade. Complete ITS-1 sequences of E . necatrix and E . mitis are reported for the first time from India. Further studies are required with more number of isolates to verify whether these differences are unique to geographical locations. [ABSTRACT FROM AUTHOR]