Objective To analyze the genetic structure and recombination characteristics of a new-ly discovered HIV-1 unique recombinant strain in Yunnan Province. Methods During a test for drug-resist-ant HIV genotypes in Yunnan Province in 2016, a recombinant fragment was found in the pol region of a HIV-1 strain isolated from a patient. Two overlapping segments of the HIV-1 genome were amplified by RT-PCR, and then the products were sequenced. Recombination analysis was performed using RIP, jpHMM and SimPlot3. 5 software. A phylogenetic tree was constructed for homology analysis by Neighbor-joining method using MEGA6. 06 software. Results A nearly full-length HIV-1 gene sequence with 8590 bp in length was obtained. Breakpoint analysis indicated that the sequence consisted of CRF01_AE and fragments of B and C subtypes. CRF01_AE was used as the backbone with B and C subtype fragments inserted. The positions were 791 to 1171 for CRF01_AE, 1172 to 2652 for C subtype fragment, 2653 to 2977 for B subtype frag-ment, and 2978 to 9380 for CRF01_AE using HIV-1 HXB2 as the reference strain. Conclusions Some new strains formed by cross-recombination of CRF01_AE and B and C subtypes were discovered in Yunnan Province in recent years. It was found that the recombination pattern of the newly discovered strain was com-plex, suggesting that close attention should be paid to the changes in epidemic trends, which was of great im-portance to understand the current prevalence and epidemic trends of HIV-1.