Two members of the familyBetaflexiviridaeassociated with yam (Dioscoreaspp.) have been described so far: yam latent virus (YLV) and yam virus Y (YVY). However, their geographical distribution and molecular diversity remain poorly documented. Using a nested RT-PCR assay, we detected YVY inD. alata, D. bulbifera, D. cayenensis, D. rotundata, andD. trifidain Guadeloupe, and inD. rotundatain Côte d'Ivoire, thus extending the known host range of this virus and geographical distribution. Using amplicon sequencing, we determined that the molecular diversity of YVY in the yam samples analyzed in this work ranged between 0.0 and 29.1% and that this diversity is partially geographically structured. We also identified three isolates of banana mild mosaic virus (BanMMV) infectingD. alatain Guadeloupe, providing the first evidence for BanMMV infection in yam.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00705-023-05809-3.