Since 2000 severe, long-lasting epidemics of bluetongue virus (BTV) have been described in Italy, caused by BTV serotypes 2, 4, 9 and 16. Vaccination programs have been applied extensively to control the infection, in spite of concerns about the potential dissemination of attenuated vaccine strains of BTV in susceptible animals. Accordingly, rapid and reliable differentiation between vaccine and field strains is paramount in routine diagnosis of BTV to evaluate the extent of this phenomenon. In the present study, we report the development of two real-time RT-PCR assays able to recognise BTV serotypes 2 and 9, respectively, and we evaluated the use of the assays for discrimination between field and vaccine strains. A total of 65 samples collected in Italy from 2000 to 2006 and diagnosed as positive for either BTV-2 or -9 were analysed by the TaqMan assays. Both the assays were found to be highly sensitive and reproducible, ensuring correct serotype characterisation and prediction of the origin of the strains, as confirmed by characterisation using virus neutralisation and sequencing.