In 1910 Morgan studied the Drosophila fly and found a mutant male fly, which expressed the trait of white eyes instead of the normal red eyes. This trait was very unusual in that species and Morgan wanted to see if the trait would be passed on to its offspring. He experimented to find if this strange trait would be inherited according to Mendel's research. First he crossed the mutant male fly with a normal female with red eyes, to observe whether the white or red eyes were dominant. The F1 generation all had red eyes, which made Morgan conclude that red eyes were dominant over white. He continued the steps of Mendel's experiment by crossing two flies from the F1 generation with each other. Out of 4252 flies in his F2 generation, 782 had white eyes but surprisingly all the flies with white eyes were also male. This strange observation puzzled Morgan to wonder why there weren't any females with white eyes. He then crossed flies from the F1 generation with the original male fly with white eyes. This cross resulted in white-eyed and red-eyed males and females, making a 1:1:1:1 ratio.

In Drosophila the sex is determined by the number of copies of the X chromosome. An individual that has two X chromosomes is female and an individual with one X chromosome, which then joins with the Y chromosome, is male. During fertilization, if the egg joins with an X sperm, the zygote is XX, which becomes female. If the Y sperm is involved in fertilization, there is a XY zygote, which develops into a male. The reasoning for Morgan's results is due to the fact that the gene for while eyes in Drosophila is located on the X chromosome and not the Y chromosome. Genes on the X chromosome that determine a trait are called sex linked. After one understands how the white-eye trait is recessive to the red-eye trait, one can easily notice that Morgan's results follow Mendel's assortment of chromosomes. Morgan's experiment has been called one of the most important events in genetics. His work with Drosophila proved Sutton's theory that Mendel's "traits" are found on chromosomes.