There have been many reports that some Listeria monocytogenes strains are able to persist in food processing facilities, creating opportunities to cause food contamination and foodborne illness. In this study, we used Whole Genome Sequencing (WGS) and subsequent analyses to investigate the genomes of 156 L. monocytogenes isolates collected from two previous longitudinal sampling studies of poultry further processing plants. The first objective was to sequence and characterize isolates to determine phylogeny, MLST-types, serotypes, and the presence of virulence and antibiotic-, stress-, and sanitizer-resistance genes. Fifty-six isolates belong to lineage I; 99 belong to lineage II. Eighteen MLST sequence types (ST) were identified, the majority of which were ST321 (n=41), ST5 (n=31), ST155 (n=27), and ST6 (n=20). All genomes contained fosX, lmo0441, lmo0919, norB, and sul antibiotic-resistance genes, 14.1% (n=22) contained aacA4, and 3.2% (n=5) contained tetM. Of the genomes, 82.7% (n=129) had 5 total antibiotic resistance (ABR) genes identified, 16% (n=25) had 6 total, and 1.3% (n=2) had 7 total. Of isolates screened, 82.7% (n=129) possessed the following genes related to stress-resistance: lmo0444, lmo0445, lmo0446, lmo0447, and lmo0448, all contained in a stress survival islet (SSI-1). The bcrA, bcrB, and bcrC genes conferring benzalkonium chloride resistance were in 73.1% (n=114) of isolates. Results provide insight about L. monocytogenes found in poultry further processing plants, including potentially high rates of ABR, stress-resistance, and sanitizer-resistance genes, and can be used to evaluate current and devise more effective L. monocytogenes control methods. The second objective of the study was to identify genes that were significantly positively or negatively associated with repeated isolation in those facilities. We found a total of 352 genes or clusters significantly associated with repeated isolation (naive P-value < 0.05 and a Bonferroni-corrected P-value < 0.05), with 180 positively and 172 negatively associated. Some notable genes/gene clusters were annotated as internalin precursors (n=28; inlJ, inlA, and inlB), CRISPR-associated (n=6), and various other genes (iap, cadA, etc.) These genes can potentially be used to further understanding of L. monocytogenes persistence in food processing environments, as markers to differentiate persistent and transient strains, or to improve methods used to clean and sanitize food processing environments.