Silybum marianum (L.) Gaertn. has been recently valorised as oilseed crop for its productivity and for the chemical composition of its oil. However, a high oleic acid oil (HO) line, which would be useful for cooking but also for biodiesel production and other industrial applications, was not found in its natural germplasm. To address this issue, an ethyl methanesulfonate-induced mutagenesis programme was implemented, and the screening of the mutagenized population led to the identification of a HO mutant line with a much higher oleic acid oil content with respect to the wild type (WT). Since Fatty Acid Desaturase 2 (FAD2) genes are responsible for the determination of oleic acid levels in vegetable oils of other species, the present research focused on the characterization of this gene family as the possible target of mutagenesis. An extremely large multigene family consisting of twenty-one unique and complete FAD2 orthologous sequences was identified in S. marianum. Sequence comparison of all the SmFAD2 genes between the WT and HO genotypes revealed a single nucleotide polymorphism (SNP) in SmFAD2–1, the only fruit-specific gene, resulting in a non-synonymous substitution in the predicted protein in the high oleic genotype. The SNP and the HO phenotype were found to perfectly cosegregate in the F2 progeny derived from the HO x WT crosses, suggesting the direct implication of this gene in the determination of oleic and linoleic acid fruit content in S. marianum fruits.