During a project investigating pea viruses in the United Kingdom (UK) and developing a workflow for high throughput sequencing (HTS) in crop surveillance, pea necrotic yellow dwarf virus (PNYDV) was identified at one site, along with pea enation mosaic virus-1, pea enation mosaic virus-2, pea enation mosaic virus satellite RNA, pea seed-borne mosaic virus and turnip yellows virus. Following an initial finding of small PNYDV contigs by RNA sequencing protocol on a MiSeq (Illumina), confirmation and prevalence testing by PCR and Sanger sequencing determined the average PNYDV prevalence to be 3%. This is the first report of PNYDV, and a nanovirus, in the UK. Initial characterisation of the octopartite genome by PCR revealed that component DNA N had a truncated sequence that differed from those previously reported. This led to confirmation testing using rolling circle amplification (RCA) into the MiSeq and then MinION (Oxford Nanopore). Sequence was obtained by both RCA-MiSeq and RCA-MinION, with the MinION producing more complete genomes than RCA-MiSeq. Data obtained from sequencing was used to provide an initial estimation of the genomic formula of PNYDV. Previous work has looked into the comparing each method, however within this study it is shown how these methods can be used together. The truncated sequence for DNA N was also found by RCA-MiSeq, RCA-MinION and confirmed by specific primers, but further work is required to understand the impact of this truncation.