Rice resistance ( R ) genes have been effectively deployed to prevent blast disease caused by the fungal pathogen Magnaporthe oryzae , one of the most serious threats for stable rice production worldwide. Weedy rice competing with cultivated rice may carry novel or lost R genes. The quantitative trait locus qBR12 . 3b was previously mapped between two single nucleotide polymorphism markers at the 10,633,942-bp and 10,820,033-bp genomic positions in a black-hull-awned (BHA) weed strain using a weed-crop-mapping population under greenhouse conditions. In this study, we found a portion of the known resistance gene Ptr encoding a protein with four armadillo repeats and confers a broad spectrum of blast resistance. We then analyzed the sequences of the Ptr gene from weedy rice, Ptr BHA , and identified a unique amino acid glutamine at protein position 874. Minor changes of protein conformation of the Ptr BHA gene were predicted through structural analysis of Ptr BHA , suggesting that the product of Ptr BHA is involved in disease resistance. A gene-specific codominant marker HJ17-13 from Ptr BHA was then developed to distinguish alleles in weeds and crops. The Ptr BHA gene existed in 207 individuals of the same mapping population, where qBR12 . 3b was mapped using this gene-specific marker. Disease reactions of 207 individuals and their parents to IB-33 were evaluated. The resistant individuals had Ptr BHA whereas the susceptible individuals did not, suggesting that HJ17-13 is reliable to predict qBR12 . 3b . Taken together, this newly developed marker, and weedy rice genotypes carrying qBR12 . 3b , are useful for blast improvement using marker assisted selection.