ABSTRACT In Listeria monocytogenes , 18 mutations leading to premature stop codons (PMSCs) in the virulence gene inlA have been identified to date. While most of these mutations represent nucleotide substitutions, a frameshift deletion in a 5′ seven-adenine homopolymeric tract (HT) in inlA has also been reported. This HT may play a role in phase variation and was first identified among L. monocytogenes lineage II ribotype DUP-1039C isolates. In order to better understand the distribution of different inlA mutations in this ribotype, a newly developed multiplex real-time PCR assay was used to screen 368 DUP-1039C isolates from human, animal, and food-associated sources for three known 5′ inlA HT alleles: (i) wild-type (WT) (A 7 ), (ii) frameshift (FS) (A 6 ), and (iii) guanine interruption (A 2 GA 4 ) alleles. Additionally, 228 DUP-1039C isolates were screened for all inlA PMSCs; data on the presence of all inlA PMSCs for the other 140 isolates were obtained from previous studies. The statistical analysis based on 191 epidemiologically unrelated strains showed that strains with inlA PMSC mutations ( n = 41) were overrepresented among food-associated isolates, while strains encoding full-length InlA ( n = 150) were overrepresented among isolates from farm animals and their environments. Furthermore, the A 6 allele was overrepresented and the A 7 allele was underrepresented among food isolates, while the A 6 allele was underrepresented among farm and animal isolates. Our results indicate that genetic variation in inlA contributes to niche adaptation within the lineage II subtype DUP-1039C.