As the HIV pandemic becomes increasingly complex and devastating in Africa, there is need to come up with better management strategies in terms of treatment, vaccine and better testing methods. However, this is getting hampered by the high diversity of Human Immunodeficiency Virus type 1 (HIV-1), which is brought about by high rate of replication and mutation. The occurrence of mutations leads to emergence of diverse subtypes and variants which are genetically related but distinguishable. Studies have associated the different subtypes with different clinical and public health consequences. In this study, molecular analysis of the Protease and Reverse Transcriptase gene sequences of the HIV-1 isolates from plasma samples collected from Gem sub county in western Kenya was done. Genes sequences generated were aligned with consensus sequences obtained from Los Alamos HIV Sequence database. Phylogentic analysis was then done using PAUPTM software, version 4.0. A total of 21 HIV-1 plasma isolate samples from Gem sub-county were taken for molecular analysis. The results showed several mutations in both Protease and Reverse Transcriptase gene regions. The phylogenetic analysis revealed, 16 (76.2%) of the 21 isolates analyzed to be subtype A, subtype D were 4 (19.0%), and the remaining 1 (4.8%) was circulating recombinant form, CRF_AD. Since this study revealed three different HIV-1 subtypes in Gem, it would be necessary to conduct a future study to find out the effect of these subtypes on the transmission, pathogenicity and the rate of HIV-1 disease progression in Gem sub-county, western Kenya.