There is a lack of information on the complete genomic profile of the hepatitis delta virus in Afghanistan. Therefore, the main objective of this study is to determine the molecular profile of complete genome of hepatitis delta virus in individuals who are positive for the hepatitis B surface antigen in the general population of Afghanistan. A total of 234 hepatitis B antigen-positive sera were analyzed by chemiluminescence microparticle immunoassay to detect anti-delta antibodies. Serologically positive samples were later confirmed by real-time polymerase chain reaction assay. Subsequently, the whole genome was amplified using two set of primers generate two partially overlapping segments and later sequenced. Phylogenetic comparison and evolutionary divergence analysis was performed with the MEGA7 software package. The coinfection rate among hepatitis B antigen carriers in Afghanistan was 2.1%. Finally, the whole genome of 4 hepatitis delta virus isolates from Afghanistan was successfully amplified, all of which were later assigned to genotype I in phylogenetic analysis. The amino acid composition of the hepatitis delta antigen and its functional motifs were consistent with genotype 1, but the subtype-specific amino acid signature illustrated different potential subtypes.