A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype–phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype–phenotype mapping using the power of Drosophila genetics. A new resource for the analysis of population genomics and quantitative traits, the Drosophila melanogaster Genetic Reference Panel is presented. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource charting the molecular and phenotypic variation in 168 fully sequenced fruitfly strains derived from a single outbred natural population. The first set of analyses of DGRP data provides insights into the genomic landscape of genetic variation, positive and negative selection, and rapid evolution of the X chromosome. The results also reveal many low frequency variants in novel loci that are associated with quantitative traits, and explain a large fraction of the phenotypic variance.