Over a decade ago, foot-and-mouth disease (FMD) re-emerged in Southern Africa specifically in beef exporting countries that had successfully maintained disease-free areas in the past. FMD virus (FMDV) serotype SAT2 has been responsible for a majority of these outbreaks. Epidemiological studies have revealed the importance of the African buffalo as the major wildlife FMD reservoir in the region. We used phylogeographic analysis to study dynamics of FMD transmission between buffalo and domestic cattle at the interface of the major wildlife protected areas in the region currently encompassing two largest Transfrontier conservation areas: Kavango-Zambezi (KAZA) and Great Limpopo (GL). Results of this study showed restricted local occurrence of each FMDV SAT2 topotypes I, II, and III, with occasional virus migration from KAZA to GL. Origins of outbreaks in livestock are frequently attributed to wild buffalo, but our results suggest that transmission from cattle to buffalo also occurs. We used coalescent Bayesian skyline analysis to study the genetic variation of the virus in cattle and buffalo, and discussed the association of these genetic changes in the virus and relevant epidemiological events that occurred in this area. Our results show that the genetic diversity of FMDV SAT2 has decreased in buffalo and cattle population during the last decade. This study contributes to understand the major dynamics of transmission and genetic variation of FMDV SAT2 in Southern Africa, which will could ultimately help in designing efficient strategies for the control of FMD at a local and regional level.