Genetic variability is a hallmark of HIV-1 infection and a significant impediment for effective vaccine development. In East Africa, multiple HIV-1 subtypes and inter-subtype recombinants coexist, and differences between these strains in disease progression and epidemic spread has been reported. Drug users have been identified as one key population that is increasingly important in driving the spread of the HIV-1 epidemic in sub-Saharan Africa but relatively little data exists on the molecular epidemiology of the virus in this population. In this study, we aimed to determine the subtype diversity of HIV-1 among drug users using limiting dilution and near full-length HIV-1 genome sequencing. So far, three near-full length genomes from plasma samples obtained from a Kenyan drug user have been generated. The resulting amplicons underwent Illumina MiSeq sequencing. Subtypes were determined using REGA and RIP tools and break point analysis performed by bootscanning in Simplot. This drug user participant had previously been classified as an A1/D recombinant based on the sequencing of the gag gene. However, full-length genome analysis revealed that the participant was infected with a complex A1/C/D recombinant. Breakpoint positions 912, 1505, 2743, 3602, 4727, 6194, 8527 and 9021 according to (HXB2 numbering). Three of the eight breakpoints were in the pol gene. Neighbor-joining trees confirmed subtype clustering in different regions of the near full-length sequencing. These data illustrate the power of employing near full-length sequencing and limiting dilution approaches to understand the diversity of HIV-1 in the phylogenetically complex epidemic of East Africa.