HIV-1 isolates are classified phylogenetically in several subtypes or clades according to env and gag coding sequences. Viral subtypes tend to cluster geographically. DNA sequences encoding the p51 subunit of reverse transcriptase were obtained by nested polymerase chain reaction from peripheral blood mononuclear cells of two HIV-1-seropositive individuals from New Delhi and three from Pune, in northern and western India, respectively. These isolates were previously characterized as subtype C according to their env sequences. Based on phylogenetic analysis, the reverse transcriptase coding region of these isolates is distinct from those of subtype A, subtype B, subtype D, and group O of HIV-1 viruses. The nucleotide divergence of these Indian pol sequences (3.3%) is similar to that of existing sequences for subtype B and subtype D viruses. This result supports the epidemiologic data of a more recently introduced HIV-1 epidemic in India. Based on the corresponding env sequences, the pol sequences described in this report are subtype C.