SummaryHuman leucocyte antigen (HLA) genetic characteristic of different ethnic minorities would be useful for tracing the origin of modern human HLA matching in transplantation and disease associations. In this study, we reported HLA‐A, ‐B, ‐C and ‐DRB1 alleles and haplotypes in the Bulang and Hani populations of southwestern China using a high‐resolution polymerase chain reaction‐Luminex (PCR‐Luminex) typing method. A total of nine HLA‐A, 22 HLA‐B, 13 HLA‐C and 18 HLA‐DRB1 alleles were identified in the Bulang population, and 11 HLA‐A, 25 HLA‐B, 14 HLA‐C and 19 HLA‐DRB1 alleles were in the Hani population. Compared with other populations, the predominant A*1101‐B*1502‐DRB1*1202 haplotype in the Bulang and Hani populations was also common in Jinuo, Wa, Dai, Maonan and Vietnamese populations. The distribution of HLA genes indicate that Bulang and Hani populations belong to the Southeast Asia group and they have maintained their original genetic characteristics and kept a long genetic distance from other populations owing to founder effects and subsequent geographic isolation. In addition, the close relationship among ethnic groups in Yunnan province and the Thai and Vietnamese populations were confirmed, whereas the Mon‐Kmer‐speaking populations shared other common HLA alleles and haplotypes compared with other linguistic groups.