Genetic characterisation of two pathogens, namely foot and mouth disease (FMD) virus and Mycobacterium bovis, isolated from African buffalo (Syncerus caffer) in southern Africa was used to determine the origin of buffalo in situations where the source of infection was obscure. By determining the phylogenetic relatedness of various FMD virus isolates using partial sequencing of the main antigenic determinant, VP1, the origin of buffalo moved illegally to the non-endemic region of South Africa was traced to the Kruger National Park (KNP) where FMD is endemic in the buffalo population. Comparative analysis of the 'genetic fingerprints' of bovine tuberculosis isolates from buffalo and cattle has aided in tracing the original source of infection of buffalo populations in the KNP. Furthermore, these analyses have assisted in tracing the origin of infected animals that have been moved to other parts of South Africa.