Nucleotide sequences of the VP1 coding region of foot-and-mouth disease viruses (FMDVs) obtained from FMD outbreaks in Eastern Uganda in April 2008 and in Northern Uganda in January 2009 were determined. Comparison of these VP1 nucleotide sequences with those of other FMDVs indicated the viruses from these outbreaks in the two regions belonged to FMDV serotype O. Bayesian Phylogenetic analyses of these sequences showed that the viruses from the two regions were closely related and belonged to topotype EA-2. Therefore the outbreaks in the two regions were due to the same serotype and strain indicating introduction of the virus from a single source. It is likely that the outbreaks in Northern Uganda were introduced from the Eastern region particularly across Lake Kyoga. This has significant implications on the effectiveness of FMD control measures in Uganda.