Several Prosopis species and provenances were introduced in Kenya, either as a single event or repeatedly. To date, naturally established Prosopis populations are described as pure species depending on site, despite the aforementioned introduction of several species within some sites. To determine whether naturally established stands consist of a single or mixture of species, six populations from Bamburi, Bura, Isiolo, Marigat, Taveta and Turkwel were compared for relatedness with reference to Prosopis chilensis, Prosopis juliflora and Prosopis pallida using random amplified polymorphic DNA markers. Cluster analysis based on Nei’s genetic distance clustered Kenyan populations as follows: Marigat, Bura and Isiolo with P. juliflora, Bamburi with P. pallida and Taveta with P. chilensis, whereas the Turkwel population is likely to be a hybrid between P. chileneis and P. juliflora. Four populations had private markers, revealing germplasm uniqueness. Expected heterozygosity tended to be larger for Kenyan populations (ranging from 0.091 to 0.191) than in the three reference (ranging from 0.065 to 0.144). For the six Kenyan populations and two P. juliflora provenances from the Middle East, molecular variation was larger within populations than between population. Higher molecular variance among populations is attributed to their geographical separation and the low variation within populations is due to gene flow between individuals within a population. Overall, this study shows that (1) the Kenyan Prosopis populations are genetically isolated, (2) multiple introductions enhanced genetic diversity within sites and (3) P. juliflora and its hybrid are the most aggressive invaders.