Inactivated vaccines against foot andmouth disease gathered from different manufacturers were screened by various methods.Gene VP1 RNA in live virus, inactivated vaccine and inactivated virus were isolated, RTPCR 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 Footandmouth Disease virus.