Foot-and-mouth disease virus (FMDV) is a positive-sense RNA virus which has caused severe damage to world-wide livestock industry. The extensive genetic and antigenic diversity observed in the evolution of FMDV is generally the obstacle for controlling the disease. The homologous recombination, as a significant force driving the evolution of virus, has also effect on the epidemiological trait of FMDV. However，the role of homologous recombination in the diversification of FMDV in China has not investigated. So it is necessary to study the homologous recombination underlying the evolution of FMDV to control FMD. Based on a sound evolutionary framework, molecular evolutionary analysis was used to identify the putative recombinants. All complete FMDV genomes from China were respectively retrieved from GenBank. Homologous recombination was identified using Simplot program. Phylogenetic relations were analyzed to determine the recombination events among these FMDV isolates by using MEGA 4. The isolates O/NY00, O/China/1/99Tibet, O/Tibet/CHA/99, O/OMIII and O/ES/2001 among 16 FMDVs were identified as putative recombinants by analyzing the FMDV genomic sequences extracted from GenBank. The recombination events frequently happen between serological type Asia1 and O which are endemic FMDV circulating in China, suggesting frequent cross infection of FMDV in China. This situation further makes controlling FMDV in China more difficult. Moreover, serotypic conversion of FMDV between Asia1 and O was detected to be due to homologous recombination. These results provided clues for understanding the antigenic and genetic diversification in FMDV, and shed lights on the potential vaccination and treatment of FMD.