Polyphenic traits are widespread, but compared to other traits, relatively few studies have explored the mechanisms that influence their inheritance. Here we investigated the relative importance of additive, nonadditive genetic, and parental sources of variation in the expression of polyphenic male dimorphism in the mite Rhizoglyphus echinopus, a species in which males are either fighters or scramblers. We established eight inbred lines through eight generations of full-sibling matings, and then crossed the inbred lines in a partial diallel design. Nymphs were isolated and raised to adulthood with ad libitum food. At adulthood, male morph was recorded for all male offspring. Using a Cockerham–Weir model, we found strong paternal effects for this polyphenic trait that could be either linked to the Y chromosome of males or an indirect genetic effect that is environmentally transmitted. In additional analyses, we were able to corroborate the paternal effects but also detected significant additive effects questioning the Cockerham–Weir analysis. This study reveals the potential importance of paternal effects on the expression of polyphenic traits and sheds light on the complex genetic architecture of these traits.