An interspecific cross (BC 1) involving a species with one of the biggest genomes in Coffea genus (C. heterocalyx (HET), qDNA = 1.74 pg) and a species with a medium genome size (C. canephora (CAN), qDNA = 1.43 pg) was studied using two types of molecular markers, AFLPTM and SSR. One hundred and eighty eight AFLP bands and 34 SSR primer pairs were suitable for the mapping. The total map length was 1360 cM with 190 loci distributed on 15 linkage groups. The results were compared to the results obtained previously on an interspecific BC 1 progeny involving a species with a medium size genome (C. liberica var. dewevrei, DEW) and a species with one of the smallest size genome (C. pseudozanguebariae, PSE). They are discussed considering three main points: 1) the interest of the different markers type, 2) - the genomic distribution of AFLPs and SSR markers and 3) - the relation between AFLP polymorphism and the genome size.