One of the major advantages of AFLP markers [26] is that they allow the simultaneous analysis of large numbers of marker loci throughout the genome. This feature is especially useful in sugar cane and its relatives as almost all species of Saccharum and Erianthus are highly polyploid (Saccharum: 6x ! 12x; Erianthus: 2x ! 6x), with large chromosome numbers [21,27].