Oral manifestations of HIV infection can be an early sign of the disease and may indicate progression to AIDS. Although antiretroviral therapies, especially highly active antiretroviral therapy (HAART), have reduced the prevalence of HIV-related oral lesions, ongoing updates in diagnosis and treatment are essential due to the extended life expectancy of individuals living with HIV. Periodontal disease is a significant concern in these patients, influenced by altered immune responses and microbial dynamics, though the mechanisms are not fully understood. This exploratory study aimed to investigate the oral microbiota and periodontal disease prevalence in HIV-positive individuals by analyzing subgingival plaque samples from 24 patients. We identified 12 bacterial species using Polymerase Chain Reaction (PCR) and amplicon sequencing. Seven species were detected, with Filifactor alocis, Tannerella forsythia, and Porphyromonas endodontalis being the most common. Porphyromonas gingivalis was present in only 13.6% of samples, while T. forsythia was found in 58.3%. Genetic diversity was also observed in P. endodontalis and Selenomonas sputigena amplicons, with specific single nucleotide polymorphisms (SNPs) identified in both species. These results highlight the complex microbial interactions in the oral environments of people living with HIV, emphasizing the need for personalized diagnostic and therapeutic strategies for managing oral health in this population.