Campylobacter is the leading cause of bacterial gastroenteritis worldwide. The most prevalent species, C. jejuni, is a strict microaerobic, capnophilic, and thermotolerant pathogen. Given its growth requirements, the ability of C. jejuni to persist in food environments and be transmitted throughout food processing has long puzzled scientists. This study aimed to compare the different genetic profiles of C. jejuni strains, isolated in Luxembourg, at the core genome (cg) and whole genome (wg) levels to elucidate its genetic population structure. Using phenotypical assays in controlled conditions and functional genomics analyses from wgMLST data, the study also investigated the possible link between phenotypic traits and emergence or persistence of genotypes. A high concordance in strain clustering was observed between genomic lineage classifications and the epidemic and endemic signals, regardless the three cgMLST typing schemes used. The higher genome stability within genomic lineages supports the hypothesis of a clonal expansion with monomorphic patterns over time and sources. A high correlation was observed between phenotypes and host-specific or generalist clonal complexes for oxidative stress, adhesion to inert surfaces, biofilm formation, and acclimation to aerobic conditions responses. These data allowed the establishment of metaphenotypes specific to the genomic lineages. Functional genomic analysis revealed factors that may contribute to the spatiotemporal survival of recurrent strains. These results also suggest the selection of better-adapted and persistent C. jejuni strains to environmental stresses throughout the transmission to human. ; CampylOmic