Biomolecular tools are widely employed in conservation genetics and wildlife management, as they provide essential information for assessing population status, guiding conservation strategies, and supporting management decisions. These tools are particularly effective in addressing a range of research questions, including the assessment of genetic variability, the characterization of population structure, individual identification, and the detection of hybridization events. In this study, we applied a panel of 4,472 high-quality genome-wide Single Nucleotide Polymorphisms (SNPs) in 78 samples belonging to the species Lepus corsicanus, Lepus timidus and Lepus europaeus, with the aim of evaluating their diagnostic efficiency in species assignment and hybridization detection compared to a previously tested set of 13 microsatellite loci (STRs). The results revealed strong concordance between SNPs and STRs, with no significant differences in their overall discriminatory power for species identification or detection of recent (F1) hybridization events. However, SNPs showed greater sensitivity in identifying recent backcrosses, a context in which STRs proved ineffective, making SNPs more suitable for detecting signals of introgression. These findings confirm that, a relatively low-density panel of SNPs can enhance the robustness and precision of genetic assessments, particularly in taxa with complex evolutionary histories or in anthropogenically managed populations.