Fruit quality is determined by numerous genetic factors that affect taste, aroma, shape, color, texture, nutritional value and shelf life. To unravel the genetic component involved in regulating the metabolic pathways behind these traits, relationships between genotypes, metabolites and gene expression are being studied. The research strategy is based on a population of recombinant inbred lines (RILs) of melon (Cucumis melo) derived from two phenotypically and genetically diverse parents (‘Dulce’ and ‘PI414723’). This population resource has been mapped with over 800 molecular markers, allowing for association analyses with fruit quality, metabolic traits and gene expression QTLs. Metabolic data are being collected using both targeted (sugars, organic acids, carotenoids, ethylene, chlorophyll, volatiles) and non-targeted methods of metabolomic analyses. Presently, transcriptomic data are being obtained from mature fruits of the RIL population, using the Illumina/Solexa sequencing technology. In addition, RILs that differ in sucrose accumulation were selected for further transcriptomic and metabolomic analyses in different stages of fruit development to identify genes controlling sucrose accumulation in melon. Genes showing expression patterns that are associated with variation of particular metabolites or fruit quality traits among the RILs will represent candidates for the molecular mechanisms that underlie these traits. The functions of identified genes will be further confirmed by co-segregation analysis in advanced segregating populations and by association studies based on a broad genetic collection.