Speciation is facilitated by ‘magic traits’, where divergent natural selection on such traits also results in non-random mating. In animal populations, diet is a potential magic trait because selection for divergence in consumed food may contribute to assortative mating and therefore sexual isolation. However, the mechanisms causing positive diet-based assortment are largely unknown. Here, using diet manipulations in a sexually imprinting species of mouse, Peromyscus gossypinus (the cotton mouse), we tested the hypothesis that sexual imprinting on divergent diets could be a mechanism that generates rapid and significant sexual isolation. We provided breeding pairs with novel garlic- or orange-flavored water and assessed whether their offspring, exposed to these flavors in utero and in the nest before weaning, later preferred mates that consumed the same flavored water as their parents. While males showed no preference, females preferred males of their parental diet, which is predicted to yield moderate sexual isolation. Thus, our experiment demonstrates that sexual imprinting on dietary cues learned in utero and/or postnatally could facilitate reproductive isolation and potentially speciation.