Rabies is a prevalent and re-emerging disease in South Africa particularly in rural areas with high human densities. Outbreaks are frequently reported in the north and eastern parts of this country, probably an indication of inadequacy in the control of the disease. Following the 2005/2006 outbreak in Limpopo, we undertook an analysis of case surveillance data and genetically characterized 18 rabies viruses, all recovered from domestic dogs. Although rabies prevalence gradually declined annually from 2007, dog rabies still remains a public and veterinary health hazard in this region. Sylvatic rabies cycles are maintained by the black-backed jackal species in specific ecological conditions in the northwest of the province (Waterberg area), unlike in the north and east (Vhembe and Mopani districts, respectively), where spillover of infection between dogs and jackals is likely to predominate. Genetic analysis demonstrated that the rabies virus strain currently circulating within dog populations in Limpopo province is the same variant responsible for the 2005/2006 rabies outbreak. However, residual foci probably exist hence the observed sporadic outbreaks. These data further underline the value of continuous and sustainable dog immunization in controlling rabies.