More than a century after the rediscovery of Mendel’s law, we still understand relatively little about the spectrum of the genetic complexity of traits. This lack of knowledge constitutes a gap in our basic understanding of how genotype determines phenotype. To obtain a comprehensive picture of the genetic complexity spectrum, we performed a species-wide survey of the inheritance patterns of a large number of traits using the Saccharomyces cerevisiae yeast model system. We performed systematic crosses between the laboratory strain (Σ1278b) and 41 diverse natural isolates covering a high genetic divergence. We quantitatively measured the fitness variation in the offspring for each cross across a large panel of stress conditions. By analyzing the distribution and the segregation of the more than 1,100 cross/trait combinations, we obtained the first estimation of the number of cases showing a Mendelian inheritance pattern within a natural population. Our results showed that 8.9% (98 out of 1,105 cases) are monogenic traits with Mendelian inheritance. Using mapping strategies combined with next-generation sequencing, we then precisely identified the genomic loci involved in the observed Mendelian traits. Interestingly, the identified Mendelian loci are not randomly distributed but rather genetically linked, leading to co-segregating phenotypes. In addition, we traced the phenotypic effect and genetic inheritance of one monogenic allele we characterized across multiple genetic backgrounds. Interestingly, increased genetic complexity was observed in 30% of the cases, with significant deviations from the Mendelian expectation. Our results clearly show that monogenic mutations might have different phenotypic outcomes with different inheritance patterns ranging from a Mendelian to a complex inheritance, including cases with intermediate levels of complexity. Overall, these data and analysis provide, for the first time, a comprehensive picture of natural genetic variants contributing to the onset of Mendelian traits, and illustrate the extent to which different genetic background could impact the inheritance pattern of these traits in a continuous way in terms of complexity. In fact, when taking into account the natural population diversity, the hidden complexity of traits could be substantial, perplexing the phenotypic predictability even for simple Mendelian traits.