Listeria monocytogenes remains a major challenge in the food industry. However, data on its genetic variability and the gene markers associated with persistence in food production environments are still limited. To expand current knowledge on the diversity and persistence of L. monocytogenes in the cheese production chain, 194 isolates collected over a 24-year period from 50 cheese processing facilities in Switzerland were characterized using WGS-based analyses. The isolates were classified into 23 different clonal complexes (CCs) with CC3, CC1 and CC101 being the most prevalent. Notably, 7 isolates were first described here for the first time as new sequence types. Seven additional isolates belonging to CC1, subtyped as ST1 and CT5518, clustered with the strain responsible for the first widely known listeriosis outbreak occurred in Switzerland during the eighties, which resulted in a high number of casualties. CC1 isolates were mostly associated with soft cheese and artisanal production, whereas CC3 isolates were more frequently isolated from hard and semi-hard cheeses, as well as from industrial and ripening facilities. Regarding persistence, some CC101 and CC3 isolates were recurrently isolated from the same facilities over periods up to 5 and 7 years, respectively. Analyses of persistence markers revealed that the mechanisms enabling survival in cheese production environments were diverse and primarily consisted of CC-specific genomic adaptations to stressors such as salinity and pH. Notably, CC3 and CC517 strains exhibited enhanced stress tolerance associated to the presence of the Stress Survival Islet 1, while other CCs showed comparable resistance through alternative genetic mechanisms. Overall, this study provides a comprehensive long-term genomic overview of L. monocytogenes in Swiss cheese production and demonstrates that mechanisms contributing to its persistence in cheese production are primarily CC-dependent, like the presence of SSI-1 in some CCs, while the acquisition of genomic islands under selective pressures may also contribute.