Khaya senegalensis (African mahogany) is a multipurpose tree species widely distributed across West Africa and valued for its ecological, economic, and socio-cultural importance. Persistent overexploitation and habitat degradation threaten forest tree species, resulting in the loss of biodiversity, genetic diversity, and other valuable genetic resources across the Mahogany range. Systematic germplasm collection and molecular assessment of genetic relationships are essential for sustainable management, and utilization of K. senegalensis genetic resources. Similarly, promising landraces for breeding programmes and conservation efforts are dependent on identification of the species. The dataset presents the rbcL-based intraspecific genetic diversity and population structure of 19 K. senegalensis accessions collected from Nigeria. Molecular analyses revealed a relatively high level of genetic diversity among the accessions, coupled with low nucleotide variability, providing insights into the genetic composition and relationships within the species. The dataset provides molecular information that can support germplasm conservation, population management, genetic resource utilization, and future breeding programmes for K. senegalensis.