A strain of Xylella fastidiosa was isolated from an invasive alternative host species, porcelain berry. Its genetic relationship with strains isolated from a native alternative host, wild grape; a nonnative alternative host, mulberry; and other economically important hosts including cultivated grape, peach, plum, oak, maple and oleander was determined by using sequence analysis of the 16S-23S rRNA intergenic spacer region. Our phylogenetic analysis revealed that the porcelain berry strain is most closely related to the wild grape strain. These two strains are more closely related to the oak, peach, and plum strains than to the mulberry and oleander strains. They are separated from the maple and cultivated grape strains. Our data suggest that suppression of porcelain berry, wild grape, and mulberry in the vicinity of susceptible economically important hosts such as oak, peach, and plum may provide an important control measure for diseases caused by X. fastidiosa.