A cold-smoked salmon factory was surveyed for a period of 1 year (2008–2009) for the presence of Listeria monocytogenes in the processing line, processing environment, personnel, raw materials and product (cold-smoked salmon). The purpose of the study was to determine whether genetically similar strains colonise different environmental niches in the processing factory and thereby determining the possible contamination source or pathways. The processing factory was divided into four zones (1–4) based on the proximity to the samples. The overall prevalence of L. monocytogenes was 24.54% (n = 444). The L. monocytogenes contamination pattern was identified by characterising 124 L. monocytogenes isolates (obtained from this survey) by Multiple Locus Variable number tandem repeats Analysis (MLVA). The isolates were divided into 8 MLVA types (Lm a, Lm b, Lm c, Lm d, Lm e, Lm f, Lm g and Lm i). The final product (cold-smoked salmon) was contaminated with two major types of L. monocytogenes; one type originating from the raw material (Lm a) and the other type colonising the production line (Lm c) in zone 1. This suggests that, in addition to the fish processing line, L. monocytogenes contaminated raw material can progress through the production chain and result in contamination of the final product. Each zone had one dominating strain type, thus leading to the hypothesis that specific L. monocytogenes strains may be better adapted to specific environmental niches in the processing factory. The results clearly indicated the problematic sites which were the raw material, cutting board, drains, floor, conveyer belt and slicer/skinner equipment. Although, these areas would be rigorously cleaned before the start of the production, there seems to be the existence of resistant L. monocytogenes strain types. In order to minimise the problem observed in this study, new cleaning and disinfection protocols should be considered.