Diversity of a population of Xylella fastidiosa isolated from sweet orange plants showing citrus variegated chlorosis (CVC) symptoms was assessed by PCR-based techniques. Thirty-seven strains were isolated throughout the 1997 year in the orange belt of Sao Paulo State, Brazil. Strains isolated from coffee, grape, oleander and plum were also included as outgroup reference strains. PCR amplification of the spacer sequence between the 16-23S rDNA yielded one fragment of 1.2 kb. Digestion with restriction enzymes, DdeI, HinfI or Sau3AI generated identical RFLP patterns for citrus and coffee strains, which could be distinguished from the strains isolated from the other hosts. Eight RAPD primers were also used and the results showed similarity from 80 to 100% within the CVC population. Three prevalent haplotypes comprising 24 CVC strains showed a high level of similarity (95%). Strains from the other hosts clustered apart from CVC strains, forming distinct groups.