In Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.