Milk thistle [Silybum marianum (L.) Gaertn.] is used as a medicinal plant for the production of silymarin. Other than silymarin, the fruit also contains valuable compounds such as oil and protein, and the lignocellulosic biomass of this species has been positively evaluated for biogas, syngas, and energy production. Despite these positive characteristics, the plant is still marked by traits that are typical of undomesticated species. Specifically, fruit shattering at maturity severely hampers its possible utilization as a crop. Therefore, for the first time, an ethyl methanesulfonate mutagenesis program was implemented to identify milk thistle lines with reduced fruit shattering, and its effectiveness was evaluated through genome‐wide analysis. The candidate nonshattering lines were multiplied up to M6 for the validation of the favorable traits. The lignocellulosic biomass of the selected shatter resistant lines was analyzed according to compositional analysis. The natural milk thistle fruit dispersal mechanism was shown to be modulated by changing air relative humidity. Three vigorous, stable, shatter‐resistant lines were identified. This is the first report that describes milk thistle nonshattering lines. At this stage in the three lines, the morphological description and the compositional analysis of the lignocellulosic biomass indicated that shatter resistance was concomitant to changes in vegetative biomass structure and composition. This observation is compatible with the described natural fruit dispersal mechanism, and it is of interest for the design of new milk thistle crop ideotypes for the complete domestication of the species.