Phytoplasmas are associated with the lethal disease of coconut palms in Tanzania (LDT). It is a destructive lethal yellowing-type syndrome (LYTS) exhibiting differences in losses between the southern districts and the northern districts. To explain these differences, the existence of variable pathogenic strains of the LDT phytoplasma was investigated using ribosomal RNA gene PCR primers. A total of 84 samples were collected from 67 palms in 14 coastal districts of Tanzania, including the low, moderate, and high incidence areas. Of these, 38 samples were studied in detail. Detected phytoplasma rDNA was characterized by either sequencing of the PCR products and/or restriction fragment length polymorphism (RFLP). Sequence analysis of the P1/P7-primed PCR products revealed several positions of variability, making it possible to distinguish two main geographical clusters. The northern cluster included samples from Tanga region only and is associated with low/moderate disease incidence. A second larger cluster included samples from the rest of the coastline between Bagamoyo and Mtwara. Five genotypes could be identified based on mutations/deletions in the P1/P7 PCR product, two within the northern cluster, and three within the southern cluster. The geographical distribution of the two clusters and the genotypes could be related to the history of coconut introductions in Tanzania. The sequences obtained also confirm that the phytoplasmas associated with LDT are significantly different from all of the other phytoplasmas associated with coconut lethal yellowing-type syndromes worldwide, and it is proposed that these phytoplasmas should be classified into their own 16Sr group.