Multilocus selection such as truncation selection can effectively reduce mutation load. Many quantitative characters including complex genetic diseases are likely to be under this type of selection; however, direct measure of selection in natural populations remains difficult. Multilocus selection with epistasis can generate linkage disequilibrium, from which we can infer the pattern and degree of selection. Previous Drosophila studies revealed the existence of recombination load, which is the reduction of fitness by recombination. Decreased fitness through recombination can occur when there are epistatic fitness interactions; in other words, gene combinations present in adult organisms that have survived selection are superior to those generated by recombination. Thus, some natural variants are not randomly combined in an individual but are instead in linkage disequilibrium. We undertook an analysis of linkage disequilibria between polymorphisms at Drosophila chemoreceptor genes, finding many significant non-random associations and a significant excess of haplotypes composed of one frequent and one less common allele in replacement polymorphisms. These results suggest that multilocus selection plays a significant role in shaping within-species variation, particularly to reduce the frequencies of replacement variants. We could, in turn, make candidate functional connections of genes based on the linkage disequilibria generated in natural populations.