The pattern of HIV-1 subtype distribution and prevalence of transmitted drug resistance mutations (TDRM) is heterogeneous across different Brazilian regions. Little information is available about the molecular epidemiologic profile in Northern Brazil. HIV-1 protease (PR) and reverse transcriptase (RT) sequences were obtained from 97 drug-naive HIV-1-infected individuals from Amapá, one of the most isolated Northern Brazilian states, for subtype determination and analysis of drug resistance mutations. The most prevalent HIV-1 clade observed in Amapá was subtype B (74%), followed by subtype F1 (14%), BF1 recombinants (8%), subtype C (1%), CRF31_BC (1%), and CRF02_AG (1%). Only one TDRM (K103N) was detected in a single patient from our study population. This study reveals that the HIV-1 epidemic in Amapá is characterized by a high level of genetic diversity comparable to that observed in major Brazilian cities, but a much lower rate of TDRM (1%).