Data from: Evidence of high genetic diversity and significant population structuring in Vachellia tortilis (Forsk.) Galasso & Bonfi population in Kenya

Key message High genetic diversity and significant population structure of Vachellia tortilis population in Kenya has been determined using nuclear microsatellite markers. Despite wide distribution and long-distance gene dispersal of the species, geographic barriers affect its gene flow patterns. The Gregorian Rift Valley that cuts across the country is suggested to have differentiated the populations into eastern and western clusters.