Rice yellow dwarf (RYD) and sugarcane white leaf (SCWL) phytoplasmas have extrachromosomal DNAs. We isolated, by sucrose density gradient centrifugation, small DNA molecules from RYD phytoplasma, which hybridized with a cloned extrachromosomal DNA fragment of the RYD phytoplasma. The isolated molecules occurred in both circular and linear forms, and their size was estimated to be about 3.8kb. Inverse PCR method showed that the extrachromosomal DNA of SCWL phytoplasma, which was about 2.7kb, has a circular form in planta. HindIII-digests of extrachromosomal DNAs of both RYD phytoplasma and HindIII or EcoRI-digests of extrachromosomal DNAs of SCWL phytoplasma showed polymorphism among isolates collected within a single field. Hybridization tests indicated that extrachromosomal DNAs of RYD and SCWL phytoplasmas shared a considerable nucleotide sequence homology, but little homology with those of sesame phyllody phytoplasma and aster yellows-type Phytoplasmas.