Abstract: In order to develop an assay to distinguish the infection of EIAV American strains from DLV，the genetic evolution of two main gene gag and gp90 of EIAV proviral DNA were investigated during recurring febrile episodes. The gag and gp90 gene were amplified with proviral DNA from PBMC of EIAV-Argentina infected horse during four febrile episodes (23, 40, 51 and 70 days postinfection).The results showed that the gag gene was conservative during four febrile episodes, the percentages of variable nucleotide is under 1% , therefore this region can be selected to design the primers for differentiate diagnosis. The variance of gp90 gene was higher at 8％-10% , the comparison of variable nucleotide showed that mutations were not randomly distributed but delineated four variables regions, A1-A4. A1, A4 variables regions mutate just one time during four febrile episodes , while A2 mutate at third febrile episodes then recover at the fourth febrile episode. The study showed that provirus was very steady after EIAV virus integrating into the cell genome ,it offer a credible basis for PCR assay of EIAV.