The contribution of non-additive genetic effects in general, and to the evolutionary potential of populations in particular, is a topic of long-standing theoretical and empirical interest, which nevertheless remains controversial. As a consequence, the empirical study of these effects in natural populations remains scarce, which is problematic because non-additive effects are expected to modify both the adaptive potential of populations and the way we should measure it. In this study, we explored the contribution of dominance and epistasis in natural Alpine populations ofArabidopsis thaliana, for two fitness-related traits, the dry weight and the number of siliques. We first found that, on average, crosses between inbred lines ofA. thalianaled to heterosis for the dry weight, but outbreeding depression for the number of siliques. We found that heterosis for the dry weight was due to positive directional dominance. For the number of siliques, however, we found that outbreeding depression was due to the breakdown of positive directional epistasis. The implication of these results for the adaptive potential of the studied populations, as well as the use of line-cross analyses to detect directional non-additive genetic effects, are discussed.