Cassava mosaic disease caused by begomoviruses is the most widespread disease of cassava in Africa. Simple sequence repeat (SSR) genetic analysis of an F1 population of cassava was carried out to identify new sources of CMD resistance. Genomic DNA extracted from parents and progeny was amplified using polymerase chain reaction (PCR). PCR amplifications were run on polyacrylamide and agarose gels. SSR marker technology was used to identify markers linked to CMD resistance via bulk segregant analysis (BSA). One hundred and forty molecular markers from the International Center for Tropical Agriculture (CIAT) were used to screen the parents, contrasting bulks and the individuals that make up the contrasting bulks. The bulk segregant analysis produced forty polymorphic markers. Screening of the contrasting individuals with the polymorphic markers revealed four candidate markers (SSRY 238, SSRY 51, SSRY 76 and SSRY 20) linked to CMD resistance. The correlation coefficient values between genotypic and phenotypic data classes for candidate markers were generally low. The t-test value between both genotypic classes (absence of band versus presence of band) were not significant (P>0.05) in each of the four markers. The results from this study suggest that there are at least two new CMD resistance genes in the mapping population.