European pear (Pyrus communis) ‘Aihuali’ carrying the dwarf character originating from ‘Nain Vert’ was crossed with ‘Chili’ (Pyrus bretschneideri). A total of 352 F1 progenies was produced to investigate the inheritance of the dwarf trait, and 111 of these were used to develop molecular markers. Chi-square analysis showed that the character fitted a 1:1 ratio indicative of a single dominant gene, which we have named PcDw. Using a bulked segregant analysis approach with 500 random amplified polymorphic DNA (RAPD) and 51 simple sequence repeat (SSR) markers from pear (Pyrus pyrifolia and P. communis) and apple (Malus ×domestica), four markers were identified as cosegregating with the dwarf character. Two of these were fragments produced by the S1212 and S1172 RAPD primers, and the other two were the pear SSR markers KA14 and TsuENH022. The RAPD markers were converted into sequence-characterized amplified regions (SCARs) and designated S1212-SCAR318 and S1172-SCAR930 and, with the SSR markers KA14 and TsuENH022, were positioned 5.9, 9.5, 8.2, and 0.9 cM from the PcDw gene, respectively. Mapping of the KA14 and TsuENH022 markers enabled the location of the PcDw gene on LG 16 of the pear genetic linkage map.