Emerging data suggest unique features characterize the rectal microbiota of men who have sex with men (MSM) and people living with HIV (PLWH). The microbiota may have important health implications in these groups, but most studies have been conducted in the United States or Europe. This study leveraged metagenomic sequencing to evaluate relationships between rectal microbiota composition and clinical, behavioral and demographic characteristics in a cohort of Nigerian MSM. PLWH with suppressed viral load had lower α-diversity (richness) compared to people without HIV (PWoH), with similar trends for PLWH with an unsuppressed viral load. Lower α-diversity (Shannon) was associated with use of petroleum jelly lubricant for anal sex. Lower relative abundance of the genus Prevotella was seen in PLWH with a suppressed viral load versus PWoH. There were differences in abundance of the top 20 taxa associated with age, HIV status (enhanced in virally suppressed PLWH versus PWoH), lubricant use, receptive anal intercourse, and condom use, suggesting multiple clinical and behavioral factors impact the rectal microbiota. Future characterization of health outcomes associated with the rectal or gut microbiota in MSM and PLWH as well as potential interventional insights will necessitate larger, dedicated studies across diverse geographic locations.