The genetic mapping strategy is very targeted for breeding and its importance is growing with the emergence of SNPs or INDELs markers, facilitated by the genome project, especially for ESTs. Thus, in silico analysis of polymorphic SNPs in sequences related to cup quality and derive from C.arabica and C.canephora were analyzed and the polymorphisms between the two species validated for six genes (four proteases and two sucrose) from laboratory studies using PCR-RFLP technique. Thus, after confirmation of polymorphism in both parental species, 90 F2 plants derived from self an interspecific hybrid of Coffea arabica and C. canephora 4x were genotyped. After obtaining the amplified, they were digested with various restriction enzymes of four bases (Alu I, DDE I, Eco RI, Hae III, Mse I and Msp, Fnu DII, Taq I, Scr FI). Of the six genes analyzed, four of them showed 3:1 segregation in the F2 population (Cysteine8, Cysteine 5, [bêta]-Fructosidase and sucrose phosphate synthase), demonstrating the use of them for mapping.