FMD is one of the most highly contagious diseases of animals, caused by RNA virus belong to Picornaviridae family and Aphtovirus genus. A broad host range and occurrence of FMDV as seven serotypes and also intratypic antigenic variation without clear cut demarcations, which interferes with a concept of sub typing these factors make difficult conditions to diagnosis, control and eradication of disease. Therefore it is very important to characterize virus strains and monitoring the field virus to determine the relationship between field viruses and vaccine strains. The objective of this study was to characterize FMD type O, A, virus isolated from Iran between 2005 and 2006. 13 FMD type A and 6 type O viruses isolated from Iran between 2005 and 2006 were used in this study. All viruses adapted to IBRS2 cells and the clarified infected cell culture supernatants were used for typing by sandwich capture ELISA and extraction of viral RNA for RT-PCR reaction with the specific primer for each type. The PCR products were purified for sequencing. Sequence of 600 nucleotides at the 3` end of 1D gene of all samples subjected to phylogenic analysis and determine the antigenic relationship ("r" Value). All type A viruses that isolated from different province of Iran, sequenced in this study, were closely related to each other and A/iran/05 virus group. The sequencing results of type O isolated from Iran between 2005 and 2006 showed the close genetic relationship between field isolates and the Iranian vaccine strain. The result of average "r" Value detected by two dimensional virus neutralization test, for type A87IR was 0.46 (46%), type A05IR 0.78 (78%), type O Shabestar 0.81 (81%) and type O967 0.90 (90%).