Coconut significantly contributes to nutrition and livelihoods of more than 8 million Asia–Pacific households and is specifically linked to the livelihoods of more than 1.5 million people in Papua New Guinea (PNG). Coconut diversity of the region is conserved, on behalf of COGENT (International Coconut Genetic Resources Network) in PNG's international coconut gene bank (ICG), which is threatened by a new lethal phytoplasma disease, Bogia coconut syndrome (BCS). Symptoms are related to lethal yellowing type syndrome (LYTS). A phytoplasma was identified in coconuts affected by BCS of coconuts but also with the palm Areca catechu and bananas. As a necessary precursor to effective disease management, this study aimed to better understand the nature of this phytoplasma using molecular analyses of the 16S rRNA-encoding gene, ribosomal protein gene, and secA gene, to characterize its genotype and compare it with any similar known phytoplasmas associated with other LYTS from the Caribbean and Africa. In the target area near to the ICG, tissue samples were taken from coconut, areca palms, and banana plants. DNA was extracted and analyzed, and phylogenetic trees and networks then drawn up to make comparisons with the known phytoplasma genotypes associated with LYTS from Cuba, the Dominican Republic (D.R), Ghana, Mexico, Mozambique, and Tanzania. Our study showed that the same phytoplasma was consistently associated with both BCS and areca samples and the banana wilt. The same unique sequence can be considered a new, genetically distinct phytoplasma and is a new member of the LYTS group, the first one in the Asian-Pacific region.