To understand the evolutionary pathway of the multi-drug-resistant virus HIV-1 under drug-induced selection pressure, plasma from seven patients from baseline to different intervals post-treatment failure were used in RT-PCR protocols. Multiple clones were sequenced for each time point. Drug-resistant mutations were detected in five patients. Phylogenetic analysis showed that at different time points, viral sequences clustered separately and formed independent lineages. Genetic diversity decreased from 1.59 to 0.55, whereas non-synonymous/synonymous mutation ratios increased from 0.067 to 0.118, respectively. These data suggest that the virus population changed dynamically and clustered in a time point-specific manner whereas genetic diversity decreased consistently.