This paper reports the evaluation of next-generation sequencing (NGS) to detect viruses following yam propagation through tissue culture. A robust methodology for the in vitro propagation of yam genotypes was established. As in vitro plantlets are not necessarily virus-free, NGS was used to determine the presence of any Badnavirus and Potyvirus species viruses in the newly cultured plants. The advantage of NGS is that it can provide the unbiased detection of novel viruses and their complete genomes without prior input of the viral sequences. The result was the detection of two Badnavirus isolates and a novel Yam mosaic virus isolate.