High level of HIV prevalence was found in some specific areas or populations in China. Shijingshan district was one of the areas with rapid increase of newly reported HIV cases in Beijing, China. Comprehensive investigation on HIV genetic characteristics is necessary in the district. In this study, we enrolled 223 newly identified HIV-1 sero-positive drug-naive patients from Shijingshan district. The full-length , , and partial gene sequences were amplified and sequenced. Genetic characterization and transmission of drug resistance of HIV-1 were further investigated. Many stains, including CRF01_AE (48.25%), CRF07_BC (31.47%), subtype B (4.9%), 55_01B (1.40%), 59_01B (0.70%), 65_cpx (2.10%), 79_0107 (0.70%), and A (0.70%) and unique recombinant forms (URF) of 0107 (6.29%), 01B (1.40%), and 01BC (2.10%), were identified. Among 106 strains that harbor full-length PR gene, 10 (9.43%) strains contain mutations associated with drug resistance to protease inhibitors. Among 59 strains that harbor full-length reverse transcriptase (RT) gene, no strains contained mutations conferred to nucleoside reverse transcriptase inhibitors resistance and 4 strains (6.78%) contained drug-resistant mutations to non-nucleoside reverse transcriptase inhibitors. Among 58 sequences harboring full-length IN gene, 1 stain (1.72%) contained a mutation causing drug resistance to integrase strand transfer inhibitors. Our results provided detailed genetic data on HIV prevalent in Shijingshan district of Beijing, which would be helpful for understanding HIV-1 transmission among local populations.