In the present study, a total of 158 blood samples from 148 bovines and 10 dogs having a history of reproductive disorders were screened for Coxiella burnetii by trans-PCR method. In case of bovines, 6.08% (9/148) blood samples comprised of 4.54% (4/88) cattle and 8.33% (5/60) buffaloes turned out to be positive for C. burnetii DNA while all the samples from dogs (10) were found negative. Of the 9 PCR-positive bovine blood samples, the organism could be isolated only from 3 cases of buffaloes by chick embryo inoculation method. Further, to predict the homology and genetic diversity, the recovered C. burnetii isolates designated as Y1, Y3 and Y7 were partially sequenced for IS1111 gene. On phylogenetic analysis, Y3 and Y7 isolates clustered to a common node away from Y1 isolate. This study may enlighten the nature of circulating C. burnetii isolates in different parts of the world. To the best of our knowledge, this appears to be the first report describing phylogenic analysis of C. burnetii isolates based on IS1111 gene sequence.