In São Paulo State (SPS), sweet orange (Citrus sinensis) trees with huanglongbing (HLB) symptoms are infected with Candidatus (Ca.) Liberibacter (L.) asiaticus (Las) or Ca. L. americanus (Lam). However, in 2007, 3 years after HLB was first reported in SPS, some trees with characteristic HLB symptoms were found free of liberibacters, but infected with a phytoplasma of 16Sr group IX. This phytoplasma was further characterized by PCR amplification of ribosomal protein genes rpsC-rplV-rpsS and amplicon sequencing. A qPCR test to detect the phytoplasma in plants and insects was also developed on the basis of the ribosomal protein genes. The phytoplasma was transmitted from citrus-to-citrus by grafting. The 16Sr group IX phytoplasma associated with HLB symptoms in sweet orange in SPS and characterized by the above techniques was named “HLB-phytoplasma”. Although the HLB-phytoplasma is widely distributed in many municipalities of central, northern, and northwestern SPS, the number of HLB-phytoplasma-infected trees in each municipality is very small. Experiments have been undertaken to identify the origin of the HLB-phytoplasma and the source of inoculum on which a putative insect vector could become infected with the HLB-phytoplasma. In SPS, sunn hemp (Crotalaria juncea L.) is a major, widely distributed cover crop. A 16Sr group IX phytoplasma was detected in sunn hemp plants with witches’ broom and virescence symptoms, and was shown to have 16Sr DNA sequences and ribosomal protein gene sequences with 100% identity to the corresponding sequences of the sweet orange HLB-phytoplasma. Transmission electron microscopy revealed the presence of phytoplasma cells in the phloem sieve tubes of infected C. juncea stalks. These results were taken as evidence that the sunn hemp phytoplasma and the sweet orange HLB-phytoplasma were identical. Scaphytopius marginelineatus, a leafhopper frequently found in sweet orange orchards, was shown to acquire the HLB-phytoplasma efficiently from affected sunn hemp plants, but acquisition from, and transmission rates to, sweet orange were very low. On the whole, these data suggest that (i) sunn hemp is a major source of inoculum of the HLB-phytoplasma, (ii) S. marginelineatus becomes infected on sunn hemp and transmits the phytoplasma to sweet orange, and (iii) transmission from sweet orange to sweet orange occurs only rarely, if at all. 16Sr group IX phytoplasmas, very closely related to the SPS HLB-phytoplasma, have also been detected in citrus in Minas Gerais and Bahia states (Brazil) and Mexico.