In the present case study, we investigated the causes of consistently elevated histamine content in raw milk cheeses from a Swiss cheese dairy. Screenings of milk samples from 67 farmers revealed that 19.1% of the raw milk samples were contaminated with histamine-forming bacteria. Lactobacillus parabuchneri was detected in 97.4% of contaminated milk samples. The population density of L. parabuchneri was almost always below the limit of quantification of the qPCR method used. Genotyping of 469 isolates provided detailed insight into the diversity of L. parabuchneri in contaminated milks and cheeses. The results of the trace-back study clearly demonstrated that several milk suppliers were responsible for the histamine problem at the cheese dairy under study. Systematic controls of milking systems allowed persistent contamination sources of L. parabuchneri at the farm level to be identified and eliminated and thereby to reduce the percentage of contaminated milks to 8.5% within the study period.