Yams (Dioscorea spp.) are economically important, annual or perennial tuber-bearing, tropical plants. Globally yam is ranked as the fourth most important root crop by production and provides a staple food for millions of people in Africa, South America, Asia and the Pacific. In the Pacific, production and utilisation of yams is limited by several issues including diseases and the lack of genetic diversity. An important global in vitro collection of yam germplasm is conserved in tissue culture by the Secretariat of the Pacific Community (SPC) in Fiji. Evaluation of this germplasm and its distribution to within the Pacific holds the key to improved production. However, similar to other vegetatively propagated crops, yam has has a tendency to accumulate and perpetuate tuber-borne fungal and viral diseases. Although, tissue culture eliminates fungal pathogens, viruses remain an issue. As such, quarantine regulations prohibit the movement of yam germplasm from the SPC collection to other countries due to the risks associated with movement of untested and/or virus-infected material. Sensitive diagnostic tests are needed to enable the virus indexing of yam germplasm. Several different viruses are known to infect yams, but badnaviruses remain the least studied and difficult to diagnose. Rolling circle amplification (RCA) based approach has been used to characterise the diversity of badnavirus infecting Pacific germplasm. A subset of the germplasm conserved at the SPC has been screened and amplified episomal badnavirus DNA has been sequenced to better understand the diversity of badnavirus infecting Pacific yam germplasm. Full genomes of three species of yam infecting badnavirus have been sequenced. The characterisation of badnaviruses infecting yams will assist in the development of reliable diagnostic techniques and furnish germplasm centres with the tools to safely mobilise their yam collections, so that food and nutritional security can be achieved in the Pacific and other regions.