To better understand the genetic diversity and drug resistance-associated mutations of human immunodeficiency virus type 1 (HIV-1) strains isolated from 118 drug-naive individuals in Shanghai. pol genes of the patients were amplified by nest reverse transcriptase-polymerase chain reaction (RT-PCR) and nucleotide sequence. REGA HIV-1 Subtyping Tool and National Center for Biotechnology Information (NCBI) HIV Subtyping Tool were used to identify the subtypes of obtained sequences. Drug-resistance-associated mutations in protease and reverse transcriptase regions were analyzed with Stanford University HIV Drug Resistance Database. The results showed that CRF01_AE predominated in Shanghai with 48.3%, followed by subtype B (30.5%), CRF07_BC (12.7%), CRF08_BC (5.9%), and C (1.7%). Besides, one inter-subtype and inter-CRF recombinants B/CRF01_AE (0.8%) was detected. Protease inhibitor-associated primary resistance mutations were found in 2 (1.7%) cases: M46L and Q58E each. The mutations conferring primary resistance to nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) were detected in 3 (2.4%) and 5 (4.1%), respectively (NRTI: M41L、D67N、T69I/N/S、K70L、L74V、V75L、V118I、M184V、L210W/F/M/S and T215F；NNRTI: V90I、L100V、K103R/N、V106M/P/I/G、E138G/A、V179E/D/T、Y181C、G190A、H221Y、F227L、K238S和Y318F). This study reveals that CRF01_AE predominates in Shanghai. Antiretroviral drug resistance among untreated HIV-1-infected individuals is 5.9%. The monitoring of HIV-1 drug resistance mutations should be paid more attention. Acquired immunodeficiency syndrome (AIDS) patients should take drug resistance test before antiretroviral therapy in future．