The internal transcribed spacer of ribosomal RNA genes in plant trypanosomes (Phytomonas spp.) resolves 10 groups

► Sixteen microsatellites (di- or tri-nucleotide) were identified in ITS-1 and nine in ITS-2. ► Microsatellites varying in copy number are informative for groups/isolates of Phytomonas. ► Microsatellites show, Group H (Phloemicola), is well identified, distinct from all other groups. ► Phylogenetic analysis identified well-defined groups (10) with high bootstrap values (97-100). ► The isolate E.het.Vz studied for the first time, appears as different from all other Phytomonas.