While we have known that HIV causes AIDS for almost 40 years and despite numerous efforts to develop a vaccine, a vaccine to prevent HIV infection is not yet available. Currently, combination treatments with multiple antiretroviral drugs are used to keep HIV infection at bay, but due to natural evolutionary processes in HIV populations, ongoing efforts to catch up with resistance-causing mutations are necessary and there is a potential for diverse drug interactions. To better understand the evolution of protein structure and function in HIV, I studied HIV from an evolutionary perspective using molecular evolution methodology and structural bioinformatics tools. I identified potential antiretroviral target regions of five or more consecutive residues that must remain conserved in sequence and structure to avoid losing viral fitness. By targeting these fitness-critical sites, the time to onset of resistance-causing mutations for antiretrovirals should be prolonged and the need for combination therapeutics reduced. I propose that by targeting these sites the function of the proteins should be greatly affected by preventing proper assembly or function of the HIV virus. Thus, drugs targeting these sites are potential treatment options that can avoid the rapid mutation of the virus and will consequently limit the current need for multiple therapeutics. Based on my results, I propose that the target site regions in the capsid are of utmost interest as a future inhibitor target. Several of these regions in the capsid are located in close vicinity of each other and appear vital in the packing of the capsid hexamer.