Beginning in 2018, a new papaya disease occurred in Ibadan, Oyo State, Nigeria. Affected papaya trees exhibited symptoms including excessive shoot proliferation at the top of the crown, leaf mosaic and crinkling, and dieback. The disease was designated as Nigerian papaya bunchy top (NGPBT) disease. Since excessive shoot proliferation was the most characteristic symptom of the disease and it was indicative of phytoplasma infection, a polymerase chain reaction (PCR)-based phytoplasma molecular diagnostic method was employed in this study. Phytoplasmas were detected in diseased papaya samples by semi-nested PCR using phytoplasma 16 S rRNA gene-specific primers. Subsequent determination and analysis of the amplified 16 S rRNA gene sequences and phylogenetic analysis revealed that NGPBT phytoplasmas were most closely related to ‘Candidatus Phytoplasma convolvuli’ in the Stolbur (16SrXII) group. Virtual restriction fragment length polymorphism (RFLP) analysis based on the 16 S rRNA gene F2nR2 fragment showed that NGPBT strains represented a novel subgroup in the Stolbur phytoplasma group, designated as 16SrXII-O. This is the first report of a phytoplasma disease in papaya in Nigeria. Identification of the NGPBT strains not only broadened the genetic diversity of the Stolbur phytoplasma group but also signaled an expansion of the phytoplasma group's geographic distribution. Notably, two previously reported phytoplasmas associated with papaya diseases in Australia and Taiwan also belong to the 16SrXII group and exhibit symptoms similar to NGPBT disease. It would be interesting to learn how these three diseases relate to each other. Further in-depth study on weed reservoirs and insect vectors of NGPBT phytoplasmas will contribute to a better understanding of pathosystem and epidemiology of the NGPBT disease.