In sugarcane, crosses are planned between genotypes from divergent backgrounds to maximize heterosis while increasing genetic diversity in the gene pool. Sugarcane breeders have traditionally relied on pedigree records when planning divergent crosses. Faulty genealogy and inadvertent mislabeling of clones adversely complicate genetic diversity estimates that rely solely on pedigree history. Sugarcane breeders are notorious for crossing mostly parents that have attained the so-called proven cross status. That is, those parents that produce elite progenies are retained for further crossing to the detriment of newer parents as evident from the high number of vintage clones still involved in the parentage of newer cultivars (Deren, 1995). Potential parents are selected largely based on their performance as clones in advanced stage trials. Therefore, continuous selections for the same traits narrow genetic diversity to the extent that it is difficult to predict diversity based on pedigree history alone. With the advent of molecular markers, it is now possible to make direct comparison of genetic diversity at the DNA level without some of the over simplifying assumptions associated with calculating genetic diversity based on pedigree history (Brar, 2002).