Wangshuibai is an indigenous scab resistance germplasm originated from Jiangsu, China. To characterize the genetic basis of scab resistance in this germplasm, QTLs for type I and type II resistances were detected using a recombinant inbred line (RIL) population created by single seed descent from Nanda2419 × Wangshuibai and a molecular marker map of more than 4000 cM constructed using RAPD, SSR and STS markers. The major QTLs for type I resistance in Wangshuibai were mapped to chromosomes 4BL and 5AS, and those for type II resistance were mapped to chromosomes 3BS. In addition, a QTL on chromosome 2B showed association with both types of resistance. These QTLs were verified with QTL nearisogenic lines. We found, by mapping QTLs for agronomical traits in the same population, that on chromosomes 4BL and 5AS the scab resistance QTLs co-located with QTLs for plant height, thousand grain weight or flag leaf width. However, these associations could be break down by recombinant selection. We concluded that Wangshuibai is a valuable scab resistance gene resources and marker assisted selection would be of great help for its better utilization.