Background: Human Immunodeficiency virus (HIV) and malaria co-infection poses a serious health threat in sub-Saharan Africa and other endemic countries. Highly active anti-retroviral therapy (HAART) is currently used to suppress viral loads. Methods: Blood samples collected from 400 participants comprising 200 HIV sero-positive and 200 sero-negative individuals was added to EDTA sample containers. Malaria parasitemia was evaluated using standard parasitological techniques followed by PCR techniques using the Quick Load One Taq One Step Polymerase Chain Reaction (PCR) for characterization of species of Plasmodium and resistant studies using specific primers. HIV viral load estimation was done using COBAS® TaqMan® Analyzer. Results: Malaria has prevalent rate of 22.75% in the study population, while the prevalence of malaria infection among the HIV sero-positive and sero-negative is 77.0% and 23% respectively. Socio-demographic factors had no significant association with the development of resistant genes. HAART exposed individuals had prevalence of PfK13 (6.9%) and Pfmdr-1 (20.8%). Viral load was significantly related with the development of resistant genes (100%) and (86.1%) for PfK13 and Pfmdr-1 respectively. Conclusion: Unsuppressed viral load in HIV sero-positive individuals heightens the prevalence of malaria parasitaemia and increases the chances of possible emergence and spread of PfK13 and Pfmdr-1 genes.

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