Polymerase chain reaction amplification of DNA from various strains of Xylella fastidiosa with tRNA consensus primers produced three different fingerprint groups. The citrus variegated chlorosis (CVC) and mulberry leaf scorch strains were unique and readily separated from each other and all other strains tested. Internal primers were designed based on the sequence of a DNA fragment unique to the CVC strain. An assay was developed with a mixture of these primers and those reported to detect 18 strains of X. fastidiosa. The assay was used to survey citrus in Brazil. The strain identified to be the cause of CVC was found in constant association with trees with CVC symptoms. On occasion, trees with no symptoms were found to have the CVC strain; this was presumably due to presymptomatic infections. No other strains were found in this survey, and X. fastidiosa was not associated with citrus blight.