Phylogenetic analysis of the nucleotide sequence of VP1 revealed that a new isolate of foot-and-mouth disease virus (FMDV) serotype Asia 1 identified in Mongolia in 2005 was related to Chinese and Russian strains isolated during the same year. In this study, these strains were defined as East Asian strains having a common geographical origin, and the complete genomic sequence of the Mongolian strain (As1/MOG/05) was determined and compared to other strains of serotype Asia 1. As1/MOG/05 showed 100% identity with an East Asian strain from China (As1/Qinghai/CHA/05) in terms of its VP1 nucleotide sequence. However, the Mongolian strain has a four-amino acid extension in 3D that is missing from all other strains of serotype Asia 1, and which is not due to an insertion. A full genomic scan revealed that the Mongolian strain is closer to the East Asian strain As1/JS/CHA/05 than to all other strains of serotype Asia 1 in nearly all genomic regions. Within the narrow region of low similarity between the two sequences, As1/JS/CHA/05 was found to have a mosaic structure with a partial 2C fragment supposedly transferred from Hong Kong strain As1/HNK/CHA/05. The genomic mosaicism and extension detected in non-structural protein-coding regions in this study may be used to trace the origins and evolution of problematic strains of serotype Asia 1 that have arisen in East Asia since 2005.