A longstanding question in evolutionary biology is how natural selection acts on standing variation, or preexisting genetic variation in a population. Recent studies suggest that HSP90, one of the molecular chaperone proteins provides a molecular mechanism for modulating the genotype-phenotype relationship. The inhibition of HSP90 function results in increased genetic variation in broad range of organisms. Such increase in genetic variation is regarded as the result of the release of the standing variation of which phenotypic effect is hidden by normal HSP90 function. At the moment, however, characteristics of genetic variation hidden by HSP90 remains unsolved. In this study, we used genome-wide association approach to evaluate whether HSP90 modulates the genotype-phenotype relationship in Drosophila melanogaster. We quantified the outline shape of male genitalia of D. melanogaster using elliptic Fourier analysis and performed principal component analysis. We then used the first and second principal components as shape scores for genome-wide association analysis. The results are still preliminary, but we want to discuss the effect of the inhibition of HSP90 by a pharmacological inhibitor of HSP90 geldanamycin on genotype-phenotype relationships of male genital shape.