Chinese cabbage is one of the most important vegetables in the world. Identifying and distinguishing between Chinese cabbage varieties is critical to management of genetic resources, new variety testing and seed quality supervision. In this study, we screened from 205 mapped SSR markers for those that amplify stably in PCR reaction and are easily scored and relatively evenly distributed on the ten linkage groups of Chinese cabbage. 30 such makers were selected for Chinese cabbage identification. The 30 selected markers were labeled with four fluorescent dyes and allele sizing were conducted using DNA analyzers based on capillary electrophoresis and fluorescent detection. Allele sizes of same groups of samples determined using three DNA analyzers of two models were compared and analyzed. And it was found that systematic errors often occur between DNA analyzers. Values of the systematic errors depended on the markers and varied between 1 and 4 bps. Alleles of the SSR loci were named according to the length of the amplified DNA fragment determined by an ABI 3730 XL analyzer. It was proved that systematic errors can be removed by using a group of reference varieties so that repeatability and reproducibility can be ensured for results from different laboratories. Molecular data of 184 Chinese cabbage varieties were collected based on the SSR marker detection system.