Two morphological types, righty and lefty, are found in several fish species. Righty predators mainly prey on lefty prey and vice versa (called cross predation). This dimorphism is heritable in a Mendelian one-locus–two-allele fashion. The frequency of righty individuals in a population oscillates periodically. To determine the effect of cross predation on this oscillation, we constructed mathematical models that describe a genetic basis of lateral dimorphism assuming genetic drift in a one-predator–two-prey system and three trophic levels with omnivory. Both models have an equilibrium of both righty and lefty types at a frequency of 0.5. Mathematical analyses and computer simulations showed that the dimorphism is maintained and that its frequency oscillated with or without genetic drift. Large degrees of drift and high intrinsic growth rates and predation efficiencies of prey species caused the frequency oscillations to be amplified and their period to be long. When cross predation decreased as a proportion of all predation, the righty frequency of a prey species fluctuated non-periodically. These differences in fluctuation patterns were observed in natural systems. Our model suggests that both cross predation and genetic drift dictate the maintenance of dimorphism and the patterns of its fluctuations.