Coffee leaf rust (CLR) and coffee berry disease (CBD) are the most economically important diseases affecting coffee production particularly in Africa. A study was undertaken to evaluate the available coffee germplasm for resistance to CLR and CBD and to determine the genetic diversity between resistant lines and commercial cultivars in Rwanda. Screening for resistance to CBD was done using the hypocotyls inoculation test while selection for resistance to CLR was carried out using the leaf disc inoculation method. The genetic diversity was assessed using both Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeats (SSR). Genetic distances generated for each pair of varieties were subjected to cluster analysis. Results showed highly significant differences between genotypes in resistance to CLR and CBD. Additionally, commercial coffee varieties in Rwanda and CLR and CBD resistant varieties were genetically quite distinct. Crosses should be made between genetically distant susceptible and resistant varieties to derive hybrids that combine resistance with marked levels of heterosis particularly for yield.