Breeding goals of yield increases, root quality improvement, and disease resistance in cassava are considerably slowed down by biological characteristics of the crop, which includes a long growth cycle, a heterozygous genetic background and a poor knowledge of the organization of crop diversity. These factors severely hamper the speed and ease of moving around useful genes in cassava. The consequences are that cassava production fails to keep up with demand, especially in regions where over 90% of yield is consumed as food, leading to an increase in acreage of cassava fields mostly into marginal lands. The advent of molecular markers, genome studies and plant genetic transformation holds promise of providing ways around breeding obstacles in long growth cycle and heterozygous crops. A number of these new tools, including a molecular genetic map, markers linked to disease resistance genes, and marker-aided studies of complex traits now exist or are being developed for cassava at CIAT. Large scale sequencing and mapping of expressed sequence tags (ESTs) have been initiated, towards a transcript map of cassava and the implementation of the candidate-gene approach to complex trait mapping. A cassava bacterial artificial chromosome (BAC) library has also been constructed to expedite positional cloning of genes, known only by their phenotypes and their position relative to markers on a molecular genetic map and complementation studies of candidate loci. Studies of genes that control traits of agronomic importance, and their allelic diversity in nature, provides powerful tools for understanding the basis of crop performance and improvement.