Dataset on rbcL-based intra-specific diversity and population structure of (Jacq.) in Nigeria.

African locust bean () is a multipurpose leguminous tree species of nutritional and pharmacological value. The plant is widely distributed in Africa and across Nigeria's major agroecological areas (AEAs). Amidst declining cultivation and production, is genetically threatened in its natural habitats due to overexploitation, deforestation, wildfires and lack of improved tree management practices. Consequently, concerted research efforts directed towards germplasm collection and assessment of genetic relationships are imperative for conserving its genetic resources, sustainable management and selecting promising landraces for breeding programmes. The dataset presents rbcL intraspecific genetic diversity and population structure of 62 landraces in Nigeria. A relatively high level of diversity and a low degree of nucleotide variability was observed among the landraces. Relatively high values of 642 total allele sites, 601 polymorphic sites, 504 parsimony information sites, 883 total number mutations, 9 haplotypes and 0.55 gene diversity were recorded for the sequence dataset. Low values of 0.35 nucleotide diversity and 5 InDels events were also recorded for the dataset. The gene flow in this dataset demonstrated an extensive exchange of genes between the three populations of which influenced the level of genetic differentiation (Gst) between the populations. Significantly low Gst (-0.01) was recorded between the Guinea and Sudan savannah populations, a moderate value (0.03) was recorded between the Sudan savannah and Rainforest populations and a higher Gst value (0.05) was recorded between the Guinea and Rainforest populations. The dataset highlights potential evolutionary dynamics that might influence variations relevant to the breeding and conservation of in Nigeria and across its range in West and Central Africa.