Indole-3-acetic acid (IAA) production is a pathogenicity/virulence factor in thePseudomonas syringaecomplex, includingPseudomonas savastanoi.P. savastanoipathovars (pvs.) genomes contain theiaaLgene, encoding an enzyme that catalyzes the biosynthesis of the less biologically active compound 3-indole-acetyl-ϵ-L–lysine (IAA–Lys). Previous studies have reported the identification of IAA–Lys in culture filtrates ofP. savastanoistrains isolated from oleander (pv. nerii), but the conversion of IAA into a conjugate was not detectable in olive strains (pv. savastanoi). In this paper, we show the distribution ofiaaLalleles in all availableP. savastanoigenomes of strains isolated from woody hosts. Most strains encode two different paralogs, except for those isolated from broom (pv. retacarpa), which contain a single allele. In addition to the three previously reportediaaLalleles (iaaLPsv,iaaLPsnandiaaLPto), we identifiediaaLPsf, an exclusive allele of strains isolated from ash (pv. fraxini). We also found that the production of IAA–Lys inP. savastanoipv. savastanoi and pv. nerii depends on a functionaliaaLPsnallele, whereas in pv. fraxini depends oniaaLPsf. The production of IAA–Lys was detected in cultures of an olive strain heterologously expressing IaaLPsn-1, IaaLPsf-1and IaaLPsf-3, but not when expressing IaaLPsv-1. In addition,Arabidopsisseedlings treated with the strains overproducing the conjugate, and thus reducing the free IAA content, alleviated the root elongation inhibitory effect of IAA. IAA–Lys synthase activity assays with purified allozymes confirmed the functionality and specificity of lysine as a substrate of IaaLPsn-1and IaaLPsf-3, with IaaLPsf-3showing the highest catalytic efficiency for both substrates. The IAA–Lys synthase activity of IaaLPsn-1was abolished by the insertion of two additional tyrosine residues encoded in the inactive allozyme IaaLPsv-1. These results highlight the relevance of allelic variation in a phytohormone-related gene for the modulation of auxin production in a bacterial phytopathogen.