Association of chromosomal gene arrangements and allozyme loci from ten local populations of Drosophila melanogaster in Korea were analyzed to determine whether the linkage disequilibria among allozyme loci are due to the hitchhiking with cosmopolitan inversions. In all, 1,717 haploid genomes were examined for six allozyme loci on the second (α-Gpd, Adh, Mdh) and third chromosomes (Pgm, Est-6, Acph) as well as for the autosomal inversions. The six genetic loci for the enzymes were found to be polymorphic. the chromosomal inversions observed were mainly common cosmopolitan types, including In(2L)t, In(2R)NS, In(3L)P, In(3R)P, In(3R)Mo, and In(3R)C. The linkage disequilibria observed between α-Gpd and Adh and between Adh and Mdh were found to be due to the hitchhiking genomes tested were associated with α-Gpdf and AdhS. Especially, all In(2L)A chromosomes observed (11/1,717) were completely linked with α-GpdS and MdhS. In the third chromosome, statistically significant linkage disequilibrium was observed between In(3L)P and Est-6. These results indicated that the allozyme loci might have been maintained by hitchhiking with the inversions.