ABSTRACTThe chromosome sequence of “CandidatusPhytoplasma australiense” (subgrouptuf-Australia I;rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of “Ca.Phytoplasma australiense” with “Ca.Phytoplasma asteris” strains OY-M and AY-WB showed that the gene order was more conserved between the closely related “Ca.Phytoplasma asteris” strains than to “Ca. Phytoplasma australiense.” Differences observed between “Ca.Phytoplasma australiense” and “Ca.Phytoplasma asteris” strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function.