Hepatitis B virus (HBV) remains one of the most pervasive viral threats worldwide, posing a significant risk to millions. Due to the absence of proofreading activity during reverse transcription, HBV exhibits a high genetic variability. To date, ten distinct HBV genotypes have been identified globally, associated with varying disease outcomes, including progression to cirrhosis and carcinoma, as well as responses to antivirals. Consequently, genotypic analysis and molecular characterization of HBV are critical for optimizing therapeutic strategies. This study aimed to investigate the distribution of HBV genotypes among Iraqi patients and to characterize their molecular profiles. Therefore, a modified protocol was used to improve sequencing success rates in samples with low amplification yields. Results: HBV/D was predominant in the study cohort (100%). Subgenotypic analysis revealed that HBV/D1 accounts for the majority of cases (68%), followed by D3 (32%). Sequences of 16 isolates were deposited in NCBI under accession numbers PV068280; PV124387–PV124397; and PV172617–PV172620. Moreover, the analysis of antiviral resistance indicated that 47% (32/68) of HBV/D1 isolates exhibited drug resistance, with all resistant isolates showing mutations associated with Lamivudine resistance (100%), Entecavir intermediate/high resistance (81% and 19%, respectively), and Telbivudine (25%). These findings underscore the dominance of genotype D, particularly HBV/D1 among Iraqi patients. To our knowledge, this is the first local study to correlate genotypic variation with drug resistance and highlight the importance of continuous surveillance for antiviral resistance to guide effective treatment strategies.