The genetic behavior of polymorphic α-Gpd, Adh and In(2L)t in the artificial populations of Drosophila melanogaster have been examined. The allelic frequency of α-Gpdf approached an equilibrium, after 20 generations, converging toward the lower rates than that of initial value, and was lower in the populations of homogeneous genetic background than that of heterogeneous background. The results seemed to suggest that α-Gpd might be influenced by some forms of selection, such as Homo-Hetero selection under the effect of genetic background. The Adhf allele frequencies converged to frequencies very similar to the frequencies in the base populations. It might be interpreted as the results of some kind of balancing selection in laboratory conditions. The In(2L)t was more rapidly eliminated in the homogeneous genetic populations than that of heterogeneous genetic populations. These results suggested that inversion in the polymorphic populations could be better maintained than that of homogeneous populations. The linkage disequilibrium between the two loci, α-Gpd and Adh, appeared to be due to the hitchhiking with In(2L)t. Therefore, recombination rather than epistatic interaction between α-Gpd and Adh appeared to influence the linkage between these two loci.