Symptoms of leaf and stem chlorosis and plant stunting were common in sweetpotato plants (Ipomoea batatas) in farmers’ fields in two widely separated locations, Kununurra and Broome, in the tropical Kimberley region in the state of Western Australia in 2003 and 2004. In the glasshouse, progeny plants developed similar symptoms characteristic of phytoplasma infection, consisting of chlorosis and a stunted, bushy appearance as a result of proliferation of axillary shoots. The same symptoms were reproduced in the African sweetpotato cv. Tanzania grafted with scions from the plant Aus1 with symptoms and in which no viruses were detected. PCR amplification with phytoplasma-specific primers and sequencing of the 16S-23S rRNA gene region from two plants with symptoms, Aus1 (Broome) and Aus142A (Kununurra), revealed highly identical sequences. Phylogenetic analysis of the 16S rRNA gene sequences obtained from previously described sweetpotato phytoplasma and inclusion of other selected phytoplasma for comparison indicated that Aus1 and Aus142A belonged to the Candidatus Phytoplasma aurantifolia species (16SrII). The 16S genes of Aus1 and Aus142A were almost identical to those of sweet potato little leaf (SPLL-V4) phytoplasma from Australia (99.3%–99.4%) but different from those of the sweetpotato phytoplasma from Taiwan (95.5%–95.6%) and Uganda (SPLL-UG, 90.0%–90.1%). Phylogenetically, Aus1, Aus142A and a phytoplasma previously described from sweetpotato in the Northern Territory of Australia formed a group distinctly different from other isolates within Ca. Phytoplasma aurantifolia species. These findings indicate that novel isolates of the 16SrII-type phytoplasma pose a potential threat to sustainable sweetpotato production in northern Australia.