Complex traits are usually controlled by several loci and populationspecifi c alleles that necessitate the use of multiple mapping populations. Consequently, a favorable allele in one genetic background can turn out to be an unfavorable allele in another genetic background. In many cases, each of these quantitative trait loci (QTLs) explains small proportions of total phenotypic variance of the trait. QTLs controlling complex traits in stone fruits have been mapped in the three major subgenera (Rehder 1940) that comprise species of horticultural importance. These include Amygdalus (peaches and almonds), Prunophora or Prunus (apricots and plums) and Cerasus (sweet and sour cherries). The high level of genome colinearity, development of transferable simple sequence repeat (SSR) markers and availability of a Prunus reference map (Joobeur et al. 1998; Aranzana et al. 2003) have highly facilitated these efforts. However, in stone fruits, most of the successes at mapping QTLs have been reported in the more tractable diploid species that comprise peach, apricot, almond and sweet cherry, while the polyploid species including plums and sour cherries have proven to be more challenging. Nevertheless, studies have identifi ed QTLs within syntenic genomic regions underlying specifi c complex traits across stone fruits, thus lending diploid species as models for understanding some complex traits in polyploid Prunus species.