Coconut foliar decay disease is found only in Vanuatu and is caused by infection with the cixiid transmitted unassigned nanovirus, coconut foliar decay virus (CFDV). The unique ecosystem and epidemiology of the disease prompted an analysis of the circular single-stranded DNAs associated with the virus. We report that there are at least nine different replication initiator protein (Rep) encoding DNAs of about 1.3 kb associated with the disease, which are more closely related to alphasatellites than the master-Rep encoding DNAs of nanoviruses. There are also two potential capsid protein encoding DNAs of about 1.3 kb and an abundant smaller DNA about half the size of the other DNAs which is encapsidated and represents a unique type of DNA with no similarity to any of the known ssDNA viruses. The capsid protein is 24kDa in size and is most similar to that of the grapevine-infecting geminiviruses rather than to the capsid proteins of nanoviruses. Taxonomically, CFDV differs from known species in the Nanoviridae and Geminiviridae, but possibly unites features of these two families. Functionally, the significance and role of the multiple disease-associated alphasatellite-like molecules, and whether they are capable of initiating the replication of any other CFDV DNA, remains unknown. In the absence of a system for testing biological properties as developed for the nanoviruses of annual plants, analyses of the encoded Rep proteins, regulatory motifs, and hypothetical proteins may have to be the principal focus for studying CFDV replication and the disease cycle in the perennial coconut palm.