Partial coat protein sequence analysis of Cucumber mosaic virus (CMV) isolates from Vanilla tahitensis crops in French Polynesia and V. planifolia crops on Réunion Island detected several different sequence variants of CMV isolates that were related to their geographic origin. French Polynesian isolates showed high molecular variability and clustered into two subgroup IB clades and one putative subgroup IA clade. The Réunion isolates grouped into a single subgroup IB clade. Experimental inoculation with a New Zealand isolate (NZ100) belonging to the CMV-II subgroup, demonstrated that vanilla is able to be infected by a very diverse range of CMV isolates.