Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., has the potential to become a serious threat to soybean production in the USA. A novel rust resistance gene, Rpp(?)Hyuuga, from the Japanese cultivar ‘Hyuuga' has been identified and mapped to linkage group C2. Our objective for this study was to develop high throughput assays to detect single nucleotide polymorphism (SNP) markers associated with this ASR resistance gene. A recombinant inbred population consisting of 92 individuals from the cross of Dillon (susceptible lesion type) x Hyuuga (resistant lesion type) was screened using melting curve analysis of fluorescent labeled SimpleProbes targeting two SNP sites near Rpp(?)Hyuuga. A set of 32 genotypes which represent 95% of the genes in the genetic base of North American soybean and the four previously reported ASR resistance genes were also screened using the SNaPshot^TM SNP assay. The two SNP sites associated with Rpp(?)Hyuuga can differentiate the rust resistant entries from the soybean ancestral genotypes. The assays we developed to detect these two SNPs are based on melting curve analysis and provide a high-throughput and rapid SNP genotyping method which can be used to accelerate the development of Asian soybean rust resistant soybean cultivars.