Legionnaires' disease (LD) is an acute pneumonia caused by the inhalation or aspiration of aerosols contaminated with Legionella bacteria. The watery environment is considered to be the natural habitat for these bacteria. Therefore, drinking water legislation is used in the primary prevention of LD, focussing on the different water sources to which the general public is exposed. For 10 years, secondary prevention of LD in the Netherlands has been organised using an outbreak detection programme that eliminates potential sources of infection that LD patients have been exposed to during their incubation period. To evaluate the two prevention strategies, we compared the distribution of Legionella pneumophila serogroup 1 genotypes isolated from patient material (n = 179) with the distribution resulting from primary (n = 182) and secondary (n = 60) prevention actions, respectively. The sequence type profiles were generated using the HiMLST method that employs next generation sequencing. We found that genotypes collected during primary prevention differ to a large extent from those isolated from patients. Genotypes collected during secondary prevention efforts had a greater similarity to that of patient isolates, but could be further improved. Our results suggest that primary prevention is not aiming at the correct reservoir, whereas secondary prevention is only partially focussed. It seems that there is a still unknown reservoir.