Legionella pneumophila serogroup 1 is the most common etiological agent of legionellosis. We have used clinical and environmental isolates from different sources to compare their genetic variability. We have obtained the nucleotide sequence for six protein-coding loci, included in the SBT scheme for L. pneumophila, and three intergenic regions from 127 samples, 47 of environmental origin and 80 from clinical samples. Levels of genetic variability were found to be higher in the environmental than in the clinical samples, but these did not represent a mere subset of the former. Not a single case of full identity between clinical and environmental isolates was found, which raises the possibility that only a specific subset of environmental isolates is actually capable of producing infection in humans. A phylogenetic analysis of the concatenate alignment of the nine loci sequences showed four main groups, each including clinical and environmental isolates, although their distribution was not uniform among them. The comparison of each individual gene tree with the others revealed several cases of incongruence involving samples from both origins, thus suggesting the presence of recombination in the two groups.