Six hundred ninety five genomes (chromosomes 2 and 3 as a unit) were extracted from a natural population (Taenung near Seoul) of Drosophila melanogaster, and they were examined at four allozyme loci on the second and third chromosomes and for chromosomal gene arrangements on those two autosomes. these data were analyzed for the detection of linkage disequilibria. All isozyme loci examined had two alleles at appreciable frequencies, except in one case (Pgm) which was polymorphic for three alleles. Linkage disequilibrium could not be detected among any pair of isozyme genes or any pair of inversions. Some disequilbria were detected, however, between isozyme genes and polymorphic inversions. In these disequilibria, the polymorphic enzyme loci were included in or closely linked to polymorphic inversions. We argue that the nonrandom associations detected are genuine and have been explained by the assumption that the primarily neutral genes are hitchhiking on the selected inversions.