This study was conducted in five regional states of Ethiopia from January 2011 to March 2012 with the objective of identifying the serotypes of foot and mouth disease by molecular technique in Ethiopia. Epithelial tissue samples were collected from cattle and swine found in the foot and mouth disease outbreak areas of the country and submitted to the National Veterinary Institute, DebreZeit, Ethiopia and World Reference Laboratory for Foot and Mouth Disease, Pirbright, UK. Thus, virus isolation and serotype identification were performed. From a total of 59 samples, cytopathic effect was observed in 43 (72.88%) samples in BHK-21 cell culture. Serotyping of foot and mouth disease viruses were done by applying agarose gel-based RT-PCR at the National Veterinary Institute, and by cell culture ELISA at World Reference Laboratory for Foot and Mouth Disease. Serotype O was recorded throughout the country where outbreaks occurred. Regular investigation of foot and mouth disease outbreaks is important to have more detailed information on the serotypes and topotypes circulating in Ethiopia and for effective vaccine development.