Drosophila melanogaster (fruit fly) is commonly used as a model organism because it has significant properties such as short life cycles, abundance in genetic variations, relative inexpensiveness, and small body size. Mendelian traits studied were bar eye (B), apterous body (ap), and vestigial body (vg). Two crosses, (Bar × apterous) and (Bar × vestigial), the corresponding F1 and F2 generations were created according to the mating map. The goodness of fit test for the observed data against the theoretical segregation ratios was analyzed using the χ2 statistical test. The results showed that the observed segregation ratios for males and females in both crosses didn’t fit the theoretical ratios because the χ2 values were much greater than the critical χ2 value (7.82) at a 5% significant level. The causes of the disagreement could be the gene interaction and the role of modifier genes. For the Bar gene, the male penetrance was complete for both crosses. The phenomenon was due to the hemizygote status of the gene. However, incomplete penetrance and variable expressivities were observed in females for both crosses. In Bar × apterous, when Bar was in homozygotic status, the penetrance was 12.5% under wild type background of wing shape and 0.0% under apterous body background. In the heterozygotic status, the variable expressivities were 41.8% of a round eye, 15.2% of a dent eye, and 30.5% of an oval eye with wild type wing allele, whereas 33.3% of a round eye and 66.7% of an oval with apterous allele respectively. There was no dent eye fly. In Bar × vestigial, the Bar gene in homozygotic status showed 17.8% and 7.7% penetrance under the background of wild-type and vestigial alleles in females. The variable expressivities exhibited 39.8% of a round eye, 17.5% of a dent eye, and 24.9% of an oval eye with wild type winged allele, whereas 30.8% of a round eye, 42.3% of dent eye, and 19.2% of an oval eye with vestigial allele respectively. The genetic study is still an effective way to investigate the gene interaction.