Objective To screen the markers of chromosome 12, which is vacant in the Beijing local standard DB11/T828.3-2011 for genetic quality control of miniature pigs in Beijing, and to study the applicability of the local standard by comparison of two different methods for evaluation of the genetic quality of the same population. Methods According to the literature, we selected four pairs of microsatellite markers of chromosome 12 and studied the polymorphism through monitoring the genetic quality of two populations of China Agricultural University miniature pigs. We screened the highly polymorphic markers of chromosome 12, combined them with the microsatellite primers of the standard 18 pairs of chromosomes to establish the whole chromosome method. We compared and analyzed the applicability of the local standard DB11/T828.3-2011 through monitoring the genetic quality of the same population of miniature pigs with different method. The data were processed and analyzed using software Popgen32. Results All the screened four pairs of microsatellite markers of chromosome 12 were highly polymorphic (PIC>0.5). The local standard showed a chromosome coverage of 94.7%, stability of amplification of 96.0%, and certified that the China Agricultural University miniature pig Ⅲ was qualified, while the China Agricultural University miniature pig I was not qualified. When the markers of chromosome 12 were added, the whole chromosome method showed result of 100% chromosome coverage and 96.6% amplification stability, both of the two populations of pigs were certified as qualified. Conclusions The four screened markers of chromosome 12 are all highly polymorphic, and provide a support for supplement of the local standard DB11/T828.3-2011.