Farmers in southwestern Uganda grow bean mixtures to manage bean root rots caused by Pythium fungi. A survey found farmers recognize root rot symptoms and use mixtures for disease insurance. Analysis of collected bean samples found two genetic groups, with the Mesoamerican group showing more resistance to root rots. While morphological diversity was higher in the Andean group, molecular analysis found greater diversity in the susceptible Mesoamerican varieties preferred by farmers for their root rot resistance. The study indicates farmer selection practices maintain genetic diversity needed to manage this key disease.