Building on quantitative genetic analysis in fruitflies I chose to investigate the molecular genetic underpinnings of natural variation in wing shape. Shape is a complex trait demanding a multidimensional description and was adequately portrayed and quantified with the tools of morphometrics. The results demonstrate uncoupling of size and shape. Shape shows strong degree of integration over the structure, disputing hypothesis of the wing as comprised of independent modules laid down by compartmentalization. However, distinctly local shape effects are also observed in genetic correlations, complementation and association tests, arguing for a continuous distribution along an axis of integration and modularity. The identification of quantitative trait nucleotides within a QTL was pursed in a two step scheme. First I tested a set of candidate loci, implicated by QTL experiments and/or developmental roles, for contribution to wing shape. The results are consistent with segregating variation of loci in the vein-determining pathways, hedgehog (hh), decapentaplegic (dpp) and Epidermal growth factor Receptor (EGFR), impacting shape. The second step involved fine-scale mapping, by testing for associations between EGFR and wing shape in two geographic populations of D. melanogaster. The genotyping was done by sequencing 10.9 kb of the locus from 209 lines demonstrating a mostly neutral locus, possibly experiencing purifying selection. One of two alternate 5'-exons may be evolving more rapidly by positive directional selection. Linkage disequilibrium decays rapidly within EGFR increasing the resolution of association mapping. Association tests identified one site (C31365T) with sex dependent effects on wing size, significant after Bonferroni correction. Seven more sites are weakly suggested. The highest of those (C30200T) disrupts a putative GAGA factor binding element and has replicable effects on crossvein placement in three study designs. The work suggests naturally occurring polymorphisms in EGFR affecting size and shape of the Drosophila wing.