Chromosomal distribution of the mys retrotransposon was examined by in situ hybridization with a biotinylated probe. Thirty-six mice from four species of the Peromyscus leucopus/maniculatus complex were examined. Mys hybridized to every chromosome in all individuals examined. However, the pattern of hybridization was nonrandom. Mys elements were excluded from C-banding regions of the autosomes, and hybridized preferentially to G-bands. The most prominent feature of these hybridizations was the preferential accumulation of mys on the X and Y chromosomes of all four species examined. Accumulation of mys on the X is incompatible with the hypothesis that selection acting on deleterious mutations is the major mechanism regulating the copy number of this element. Rather, this supports the Langley model for containment of transposable element copy number by unequal exchange during meiosis.