| Summary: | The use of resistant cultivars is the most effective strategy for controlling coffee leaf rust caused by the fungus <i>Hemileia vastatrix</i>. To assist the development of such cultivars, amplified fragment-length polymorphism (AFLP) markers linked to two loci of coffee resistance to races I and II as well as pathotype 001 of <i>H. vastatrix</i> were converted to sequence-characterized amplified region (SCAR) and cleaved amplified polymorphic site (CAPS) markers. In total, 2 SCAR markers and 1 CAPS marker were validated in resistant and susceptible parents as well as in 247 individuals from the F<sub>2</sub> population. The efficiency of these markers for marker-assisted selection (MAS) was evaluated in F<sub>2:3</sub> and backcross (BCrs<sub>2</sub>) populations genotyped with the developed markers and phenotyped with race II of <i>H. vastatrix</i>. The markers showed 90% efficiency in MAS. Therefore, the developed markers, together with molecular markers associated with other rust resistance genes, were used for F<sub>3:4</sub> and BCrs<sub>3</sub> coffee selection. The selected plants were analyzed using two markers associated with coffee berry disease (CBD) resistance, aiming for preventive breeding. MAS of F<sub>3:4</sub> and BCrs<sub>3</sub> individuals with all resistance loci was feasible. Our phenotypic and genotypic approaches are useful for the development of coffee genotypes with multiple genes conferring resistance to coffee leaf rust and CBD.
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