Inactivated vaccines against foot andmouth disease gathered from different manufacturers were screened by various methods.Gene VP1 RNA in live virus, inactivated vaccine and inactivated virus were isolated, RTPCR amplified, cloned, cDNA sequenced and comparative analysis. The results indicate that,VP1 RNAs isolated from live virus, virus inactivated by BEI and inactivated vaccine emulsified by white oil access to all of the 813 bp specific objectives of fragments, and the expected 813 bp fragment match. Nucleotide sequence revealed that VP1 homology of the virus was 100% isolated by three methods. BEI and the emulsification process do not damage whole RNA structure of VP1. The isolated method to RNA can be used to analyse sequence of VP1 RNA, which derived from either live or inactivated Footandmouth Disease virus.