In order to investigate the infection status of equine piroplasmosis in Yanqi horse farms in Xinjiang，and to implement comprehensive prevention and control measures to ensure healthy development of horse industry in the region，five farms were selected to collect blood samples from 156 Yanqi horses for DNA detection of equine piroplasmosis pathogen. The infection status of the horses at different ages and in different sampling sites and of different genders was analyzed by SPSS Statistics 17.0，Meaglign and MEGA 11.0，meanwhile，the homology of pathogenic nucleic acids was compared and a phylogenetic tree was constructed. The results showed that 82 positive samples for equine piroplasmosis pathogen nucleic acids were detected，the positive rates of Theileria equi（T. equi），Babesia caballi（B. caballi）and their mixed infection were 33.3%（52/156），26.9%（42/156）and 7.7%（12/156），respectively. There was no significant difference（P＞0.05）in the positive rate of equine piroplasmosis in different sampling sites and the horses at different ages and of different genders. It was found that，by the analysis with Meaglign and MEGA11.0，the homologies of the obtained gene sequences of T. equi 18S rDNA and B. caballi BC-18S rRNA were from 95.5% to 100% and from 98.6% to 99.6%，respectively with the reference strain. For T. equi，its 18S rRNA gene and Ili strain（OL589505.1），with closer evolutionary relationship，were located in the same branch，but far from the strains in other regions，so was the BC-18S rRNA gene of B. caballi and Xinjiang strain（MT563457.1）. In conclusion，the disease was widely prevalent in Xinjiang，which should be further monitored，prevented and controlled. Field data was therefore provided by the investigation described in the paper for future comprehensive prevention and control of the disease.