Equine infectious anemia (EIA) is a viral disease wich affects all members of Equine species and is caused by а virus belonging to the genus Lentivirus in the family Retroviridae. This disease has a worldwide distribution, and its epizooty is registered in all continents. AGID positively reacting animals are revealed at planned serological studies in the Russian Federation from year to year. At the moment, a lot of attention is paid to control of the EIA virus prevalence, therefore, all over the world there are numerous studies to identify the virus and determine its molecular and genetic characteristics and origin. This paper presents data on the development of test systems based on PCR, which allows not only to identify the EIA viral genome in various samples of biological material, but also to carry out further sequencing the genome fragments of different EIA strains and isolates.