The Republic of Belarus reports a seroprevalence of 4.8% for hepatitis B virus (HBV) and 1.26% for hepatitis C virus (HCV), but little is known about the molecular characteristics of the circulating viruses. This study analysed 69 HBV surface antigen (HBsAg)-positive and 113 anti-HCV-positive donors attending a national reference hospital in Minsk. Among the HCV patients, 70% were co-infected with human immunodeficiency virus (HIV). Phylogenetic analysis of 12 complete genomes and 31 partial HBV sequences, as well as 78 core/E1 HCV sequences, revealed that multiple genotypes and subtypes of both viruses were circulating in Belarus. Of the HBV strains, 11.6% were genotype A2 and 88.6% were genotype D. The genotype D strains segregated into four recently described subtypes, with D2 being the most prevalent (58.1%), followed by D3 (16.3%), D1 (11.6%) and D4 (2.3%), but with inter-subtypic distances lower than the minimal 4% distance proposed to define subtypes. The 78 HCV strains belonged to subtypes 1b (53.8%), 3a (38.5%), 1a (5.1%), 4a (1.3%) and 4d (1.3%). Subtype 1b was less prevalent (45.1% vs. 70.4%) among HCV/HIV co-infected donors, while subtype 3a was more prevalent (29.6% vs. 43.1%). The relative prevalence of HBV and HCV genotypes in Belarus corresponded to the prevalence in Russia, although with a clear European influence that reflected the socio-political context of the country.