Technical Abstract: Xylella fastidiosa is a Gram negative plant pathogenic bacterium that causes almond leaf scorch disease (ALSD) and grape Pierce’s disease (PD) in California. A-genotype strains cause ALSD only. G-genotype strains cause both PD and ALSD. Little is known about how X. fastidiosa interacts with the environment. In this study, we identified a putative protease encoding locus, PD0218 (pspB), in the genome of X. fastidiosa and evaluated genetic variation that may affect gene expression or function. PD0218 contains tandem repeats of ACDCCA at the 5’ end, corresponding to TP (threonine and proline) at the N-terminus of the protein. Comparative sequence analyses of 116 X. fastidiosa ALSD and PD strains collected from seven locations in California showed that the tandem repeat numbers (TRNs) ranged from 10 to 48, suggesting that X. fastidiosa possesses a mechanism of contracting and expanding the number of tandem repeats. Differences in pspB protease gene length may be in response to different environmental conditions encountered by X. fastidiosa strains. The hyper-variable nature of TRNs indicates that estimates of genetic variation among X. fastidiosa strains based on the pspB locus may overestimate diversity in the bacterial population.