Understanding the variation of mating patterns in disturbed habitats provide insight into the evolutionary potential of plant species and how they persist over time. However, this phenomenon is poorly understood in tropical dryland tree species. In the present study, we investigated how Acacia senegal reproduces in two different environmental contexts in Kenya. Open-pollinated progeny arrays of 10 maternal trees from each environmental context were genotyped using 12 nuclear microsatellite markers. Overall, A. senegal displayed a predominantly allogamous mating pattern. However, higher multilocus outcrossing rate (tm) was found in Lake Bogoria (tm = 1.00) than in Kampi ya Moto population (tm = 0.949). Higher biparental inbreeding (t m − t s = 0.116) and correlation of outcrossed paternity (rp = 0.329) was found in Kampi ya Moto than in Lake Bogoria population (t m − t s = 0.074, rp = 0.055), showing the occurrence of mating among relatives. Coefficient of coancestry (Θ = 0.208) showed that full-sibs constitute about 21% of the offspring in Kampi ya Moto population compared to about 14% (Θ = 0.136) in Lake Bogoria population. The results demonstrate that low adult tree density of A. senegal may be promoting seed production through consanguineous mating and suggest that man-made disturbance can affect mating patterns of the species. Despite these mating differences, trees from both populations can contribute as seed source for conservational plans, and to support effective genetic conservation and artificial regeneration programs of A. senegal. We suggest collection of seeds from at least 42 and 63 trees in Lake Bogoria and Kampi ya Moto populations, respectively, to retain a progeny array with a total effective population size of 150.