In spite of the economical relevance of polyploid crops, genetic mapping of these species has been relatively overlooked. This is because of intrinsic difficulties such as the uncertainty of the chromosome behavior at meiosis I and the need for very large segregating populations. An important, yet underestimated issue, in mapping polyploids is the choice of the molecular marker system. An ideal molecular marker system for polyploid mapping should maximize the percentage of single dose markers (SDMs) detected and the possibility of recognizing allelic markers. In the present work, the marker index for genetic mapping (MIgm) of M-AFLP is compared with that of AFLP and SAMPL. M-AFLPs have the highest MIgm values (22 vs. 18.5 of SAMPL and 9.83 of AFLP) mostly because of their high power to detect polymorphism. Owing to their prevalent codominant inheritance, it is proposed that M-AFLP can be used for the preliminary identification of hom(e)ologous groups.