Plant breeders would welcome new tools to improve selection efficiency for complex traits such as improved flavor, especially since this is only one of many complex traits that a breeder has to integrate into improved cultivars. Using tomato (Lycopersicon esculentum Mill.) flavor as an example, a major obstacle to improvement is the lack of measurable traits to select for. It has been suggested that improved flavor can be achieved by increasing the soluble solids and acidity. Both of these traits are not simply inherited, but if fruit sampling is adequate, they can be measured and selected. Studies have located several molecular markers linked to high soluble solids, but some are also linked to undesirable traits such as small fruit size or low yield. Thus, the molecular markers are not being used in breeding programs at this point. Moreover, other studies have shown that flavor is also influenced by an array of aromatic volatiles. The importance of some of the volatiles has been reported, but the volatile profile that consistently results in superior tomato flavor is still not known. Molecular manipulation of a biochemical pathway has been done to increase the concentration of one volatile with positive results. However, this manipulation does not solve the overall flavor improvement problem. Furthermore, environment plays a profound role in tomato flavor, and this aspect needs to be dealt with if a branded high-quality product is to be successfully marketed. There are also flavor issues related to fruit firmness, pedicel type, and plant habit. In summary, molecular techniques may be useful in providing some incremental improvements for complex traits like tomato flavor, but more knowledge about targets to manipulate is required. There does not appear to be any cheap or easy solutions. If molecular approaches are to be commercially successful, they will have to be tied closely to a breeding program dedicated to the same goal.