Abstract: The partial intron 1, complete exon 2 and partial intron 2 of SLA-DQA gene was amplified and a uniform fragment of 341 bp was obtained in Diannan small-ear pigs (DN) and Bama miniature pigs (BM). After PCR products were purified and digested by EcoR Ⅰ and Alu Ⅰ, the results showed that the genotype frequency of BB (0.468 8) at EcoR I-RFLP site was higher than that of AB (0.375 0) and AA (0.156 3), respectively. By comparing with the allelic frequency, the predominant allele was B(0.656 3),while the inferior allele was A (0.343 7).To the Alu Ⅰ-RFLP site, the genotype frequency of MM (0.500 0) was higher than that of MN(0.321 4) and NN(0.178 6) in DN, respectively. While the genotype frequency of MN (0.485 3) was higher than that of MM (0.338 2) and NN (0.176 5) in BM, respectively. The allelic frequency of M (0.604 2) was higher than that of N(0.395 8) in two breeds. The results of χ² analysis showed that genotypes of the SLA-DQA gene in two breeds fit Hardy-Weinberg equilibrium. There are nine and seven composite genotype of SLA-DQA gene in BM and DN, respectively. Among them, the most favorable was BBMN, while the inferior was AAMN, the genotype frequency of AAMM were found to be significantly different between two pig breeds（P<0.05）. The results of genetic parameters showed that there were moderate polymorphic in exon 2 of SLA-DQA gene, the polymorphism information content (PIC) at Alu I site was higher than that at EcoR I site, the slightly higher heterozygote existed in BM than that in DN, the Nei’s unbiased genetic distance is 0.000 4 between two breeds.