Common bean anthracnose caused by Colletotrichum lindemuthianum is one of the major biotic constraints to production of French beans (Phaseolus vulgaris L.) in Kenya. This study aimed at screening French bean genotypes in relation to their response to common bean anthracnose in order to identify potential sources of germplasm for breeding. The genotypes were tested in three sites (Kakamega, Mwea and Kutus) where results revealed a significant genotype by environment interaction effect (p ≤ 0.05) which emphasizes the strong influence of the growing conditions on the expression of host resistance. Physiological characterization identified a total of 14 distinct races out of 16 successfully plated isolates, revealing a very high diversity of C. lindemuthianum in Kenya. Six races have not been reported in previous studies in the country and are considered as new races, that is, races 84, 141, 246, 515, 576 and 768. Andean race 401 was the most virulent race with a virulence index of 67% among the genotypes. Molecular analysis using six sequence characterized amplified region (SCAR) markers revealed polymorphism among the genotypes. The SCAR markers SBB-14, SH-18 and SAB-03 have shown to be useful for marker assisted selection (MAS) of the target resistance genes. This study has also identified locally improved breeding lines as potential donors for resistance breeding to C. lindemuthianum in Kenya.