Recombination contributes substantially to the genetic diversity of HIV-1, and is likely to occur in populations in which multiple subtypes circulate. Molecular epidemiological studies showed that subtype B, CRF01_AE, and CRF07_BC are currently circulating in parallel among men who have sex with men (MSM) in China, suggesting the possible emergence of new recombinants. In the present study, we identified two new HIV Type 1 unique (CRF01_AE /B) recombinant forms in this population by near full-length genomic analysis. Our data provided the first description of the near full-length genomes of these new CRF01_AE/B recombinants as well as important insights into the complexity of HIV-1 recombinant strains currently in circulation among MSM in China. These data highlight the importance of continuous surveillance of the dynamic change of HIV-1 subtypes and new recombinants among the MSM population.