The fast growing HIV-1 epidemic in South Africa is mainly caused by HIV-1 group M subtype C, spreading via heterosexual transmission. In South Africa HIV-1 subtype B and D viruses were responsible for the initial epidemic during the 1980s, primarily in the homosexual population. This study describes the full-length PCR amplification and sequencing of an HIV-1 subtype D strain recovered from plasma from a sample taken during 1990. This is only the second full-length non-syncytium-inducing (NSI) subtype D strain described. Although restricted, the subtype D strain is still being detected in the South African population.