Spiroplasma citri virus SpV1-R8A2B is a naked, rod-shaped virus with a circular, single-stranded DNA genome of 8273 bp. SpV1-related sequences were detected in the chromosomal DNA of all S. citri strains tested. Southern blot hybridization analyses revealed that several copies of most, if not all, SpV1 ORFs are present in the chromosome of S. citri strain R8A2. For further study of the integrated viral sequences, a genomic DNA library of S. citri R8A2 was constructed, and two cloned chromosomal DNA fragments containing SpV1 viral sequences were studied by comparison with the free viral genome of SpV1-R8A2B. One fragment seems to contain a full-length viral genome, while the other contains only parts of the viral genome. In both fragments, the left and right ends of viral sequences consist of 31-bp inverted repeat sequences, those which are facing each other at nucleotide 4737 in the circular viral genome. In addition, both fragments contain the SpV1-ORF3, encoding a putative transposase, immediately upstream of the right repeat. These data suggest that the SpV1-ORF3 and the repeat sequences could be parts of an IS-like element of chromosomal origin.