Bougainvillea‐potted plants exhibiting typical phytoplasma‐induced symptoms, characterized by foliar chlorosis, shoot proliferation, leaf and bract deformations, and decline were observed in commercial nurseries, located in the state of São Paulo, Brazil. In this study, PCR assays using group‐specific primers revealed that phytoplasmas affiliated with the groups 16SrI and 16SrIII were associated with symptomatic plants. Molecular analysis based on conventional and virtual RFLP patterns and similarity coefficient calculations identified these phytoplasmas as belonging to subgroups 16SrI‐B and 16SrIII‐B. Phylogenetic analysis confirmed that these phytoplasmas were closely related to representatives of both subgroups. Transmission assays using dodder supported the initial evidence that the symptoms were associated with phytoplasmas.