Sweet potato witches' broom disease caused by phytoplasmas threatens crop productivity in Fujian, China. Here we report a complete phytoplasma genome consisting of a single circular chromosome (680,179 bp with a G+C content of 29.44%) via the next-generation sequencing of sweet potato witches’ broom-infected samples. A total of 730 genes were predicted, while two 16S rRNAs were revealed to be identical to sequences in ‘Candidatus Phytoplasma australasiaticum’. Following the latest guidelines for the description of phytoplasma species, we have named the strain Candidatus Phytoplasma australasiaticum SPWBPT2024. The genome contained 33 transporters, 35 putative effectors (including SAP11 and SAP54 with multiple copies), and two potential mobile units. Analyses of published peanut and sweet potato phytoplasma genomes revealed the similarities between their effectors and the effectors in this phytoplasma genome. A motif analysis was performed to clarify the difference between the two SAP54 copies in the obtained phytoplasma genome as well as the trends in conserved motifs in other strains. In addition, metabolic pathway-related genes in three genomes were examined, revealing deficiencies in the glycolysis and pyrimidine synthesis pathways. A pan-genome analysis has revealed that the phytoplasma genome is an open genome. To gain further insights into whole-cell metabolic processes, we reconstructed draft genome-scale metabolic models (GEMs) of the genome. This study provides valuable genomic insights into this phytoplasma, characterising conserved and strain-specific SAP effectors, as well as distinct metabolic deficiencies that may help advance research to combat phytoplasma infections, including accurate diagnostics, vector transmission control and antimicrobial interventions.