In　recent　years,　immunization　with　the　S2　live-attenuated　vaccine　has　been　recognized　as　the　most　economical　and　effective　strategy　for　preventing　brucellosis　in　Inner　Mongolia,　China.　However,　there　are　still　challenges　related　to　vaccine　toxicity　and　the　inability　to　distinguish　between　vaccine　immunization　and　natural　infection.　Therefore,　in　this　study,　we　developed　a　digital　droplet　polymerase　chain　reaction　(ddPCR)　assay　based　on　single-　nucleotide　polymorphism　(SNP)　loci　to　identify　wild　Brucella　strains　and　S2　vaccine　strains.　The　assay　demonstrated　excellent　linearity　(R-2　＞　0.99)　with　a　lower　detection　limit　of　10　copies/mu　L　for　both　wild　and　vaccine　strains.　Additionally,　the　ddPCR　assay　outperformed　the　real-time　fluorescent　quantitative　PCR　(qPCR)　assay　in　screening　50　clinical　samples.　We　have　established　an　effective　and　highly　sensitive　ddPCR　assay　for　Brucella,　providing　an　efficient　method　for　detecting　and　differentiating　wild　strains　of　Brucella　from　the　S2　vaccine　strain.