Technical Abstract: Fresh tomato fruit flavor is the sum of interaction between sugars, acids and a set of approximately 30 volatile compounds synthesized from a diverse set of precursors, including amino acids, lipids and carotenoids. Some of these volatiles impart desirable qualities while others are negatively perceived. As a first step to identify genes responsible for synthesis of flavor-related chemicals, we have sought to identify loci that influence the chemical composition of ripe fruits. We used a genetically diverse but well defined Lycopersicon pennellii RIL population (Eshed and Zamir, 1995). Because L. pennellii is a small green-fruited species, this population exhibits great biochemical diversity and is a rich source of genes affecting both fruit development (Fridman et al. 2004) and chemical composition (Causse et al., 2004; Schauer et al. 2005). Here, we use this population to identify multiple loci affecting the composition of chemicals related to flavor. We identified 25 loci that are significantly altered in one or more of 23 different volatiles and four altered in citric acid content. Linked molecular markers should be useful for breeding programs aimed at improving fruit flavor. In the longer term, genes responsible for controlling levels of these chemicals will be important tools for understanding the complex interactions that ultimately integrate to provide the unique flavor of a tomato.