South America is considered to have a low prevalence of hepatitis B virus (HBV) infection, although areas with a relatively high prevalence have been identified in northern Brazil. Few epidemiological studies of populations at risk of HBV infection are available for this region. Given this, in the present study, we investigated the prevalence of HBV and the factors associated with infection among illicit drug users (DUs) in the Marajó Archipelago, northern Brazil. In this cross-sectional study, we collected samples and epidemiological information from DUs in 11 municipalities of the Marajó Archipelago. The diagnosis was established by ELISA and real-time PCR; and genotyping was done by multiplex real-time PCR. Statistical modeling was based on simple and multiple logistical regressions with the Hosmer-Lemeshow test. The mean age of the 466 DUs was 28.4 years, and most were male. The most-consumed illicit drugs were crack cocaine and marijuana. In all, 171 DUs were exposed to HBV, with genotypes A, D and F being identified. The factors associated with higher frequencies of HBV infection were (i) male gender, (ii) age above 35 years, (iii) anti-HIV positivity, (iv) tattoos, (v) the use of injected drugs, (vi) the use of illicit drugs for more than 3 years, (vii) sexual relations without protection, (viii) sexual relations with another DU, and (ix) more than 10 sexual partners in the past 24 months. In summary, this study provides important insights into the dynamics of HBV infection among DUs in the Marajó Archipelago. We hope that these findings will contribute to the development of strategies, actions and public health policies aimed at preventing and controlling this viral infection more effectively.