Background: Reports on HBV genotype I in Vietnam, Laos, northeastern India, and China are limited and thus, no studies have examined HBV genotype I quasi species with coexistence of HBsAg and anti-HBs. Methods: The current study reports on an HBV genotype I quasi species isolated from a male patient (AO2) showing coexistence of HBsAg and anti-HBs. The researchers identified a HBV strain isolated from a CHB patient from Zhaotong city, Yunnan province, China, who was infected with HBV genotype I and presented HBsAg and anti-HBs coexistence. In an effort to elucidate the mechanism underlying the coexistence of HBsAg and anti-HBs in this patient, the researchers performed full-length genome amplification, and the HBV strain was cloned to conduct a comprehensive analysis of mutations and to analyze quasi species variation in relation to the coexistence of HBsAg and anti-HBs. Results: The analysis indicated that the pre-core/core had the highest diversity, and HBsAg and MHBsAg accumulated more nonsynonymous mutations than synonymous mutations. Phylogenetic analyses and genotype identification suggest thatAO2 was infected with a putative genotype I strain. Unusual deletions of PreS (11 of 16 clones (69%) in PreS1) and amino acid variants of HBsAg (11 of 16 clones; 69%) were observed in the AO2 quasi species that were associated with the coexistence of HBsAg and anti-HBs and other clinical features, thus conferring resistance to current antiviral therapies. Further functional studies are needed to assess the correlation between these variants and the coexistence of HBsAg and anti-HBs. Conclusions: The propensity for PreS1 deletions and the complexity of HBsAg variants in HBV isolates from a single patient infected with HBV genotype I could explain the coexistence of HBsAg and anti-HBs and the resistance to current antiviral therapies.