Certain pathogens evolve with their hosts in a stepwise arms race of virulence and resistance, mediated by one or a few genetic loci in their genomes. Other pathogens may retain the ability to colonize hosts through multiple small genetic changes, which do not necessarily occur solely at loci under selective pressure. The bacterial plant pathogen Xylella fastidiosa lacks classic indicators of pathogenicity such as a type III secretion system, which makes the identification of its virulence mechanism challenging. We tested the hypothesis that quantitative differences in virulence between pairs of X. fastidiosa isolates were correlated with their respective genetic distances. Isolates from two different X. fastidiosa subspecies were genetically typed using 20 loci, generating information on the genetic distance among pairs of isolates. Virulence data were obtained by determining the impact of these genotypes on the phenotype of alfalfa plant hosts. Results show significant or marginally significant correlations with respect to differences in infection level and alfalfa stunting, suggesting that genetic distance partially explains plant phenotypic differences in virulence among X. fastidiosa isolates. Furthermore, the data demonstrate substantial amount of phenotypic variation among X. fastidiosa isolates within subspecies fastidiosa and multiplex.