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In the last few decades, populations of wild boars have been spreading throughout Europe. This expansion is problematic because of conflicts with human activities and/or sanitary reasons. Thus, the need to develop tools to understand wild boar populations’ increase as well as to manage efficiently their populations appears crucial but challenging. As ancestor of the domestic pig, one of the main issues associated with this population spread is the possible hybridization between the two subspecies which complicates the identification of pure individuals. In this study, we propose a set of 20 single nucleotide polymorphism (SNP) markers, allocated in two 10-plexes, selected in order to identify the two subspecies. The multiplexes were validated on reference populations of wild boars and domestic pigs in order to assess their polymorphism and their discriminative power. The selected markers allowed for an exacerbated differentiation between the wild boars and the domestic pigs compared to other studies and thus allows for an efficient identification of species. The low size of this panel of 20 SNP markers makes it a tool compatible with economic constraints associated with wildlife management compared to tools based on chips.