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Weak selection is maintaining the Drosophila americana X/4 fusion chromosomal frequency cline. The gene(s) harbouring the advantageous variant(s) that is responsible for the establishment and maintenance of this chromosomal frequency gradient must be located in a region of the X and/or 4th chromosome that is genetically isolated between the X/4 fusion and non-fusion forms. The limits of these regions must thus be determined before an attempt is made to identify these genes. For this purpose, the correspondence between the D. virilis X and 4th chromosome genome scaffolds sequence and the D. americana gene order was established. Polymorphism levels and patterns at seven genes located at the base of the D. americana X chromosome, as well as three genes located at the base of the 4th chromosome, were analysed. The data suggest that the D. americana X/4 fusion is no more than 29000 years old …