Species conservation is a difficult task, especially when it involves taxonomically complex groups, where conventional species identification fails. Such is the case of the Vanilla genus, which comprises 18 leafless species spread across the Caribbean, Asia and the south-west Indian Ocean region. In Madagascar, leafless vanillas are under constant threat from deforestation and harvesting for medicinal purposes. They have strong morphological similarities and chloroplast DNA failed to differentiate them. We therefore used an integrative approach to resolve the taxonomy of these species and provided the information needed to plan their conservation. Phylogenetic analyses based on the ITS region combined with microsatellite genetic structuring and morphological comparison confirmed the presence of seven species in Madagascar, two of which are newly described. Genetic analyses and information on reproductive biology suggest that V. atsinananensis, V. allorgeae and V. decaryana are threatened by low population density, loss of interaction with pollinators and high inbreeding, respectively. Based on spatial distribution modeling, V. bosseri and V. perrieri are of least concern as they are widespread on the west coast. V. madagascariensis and V. humblotii are vulnerable due to their restricted potential distribution. To protect these wild species, ex situ and in situ conservation with a strong involvement of local communities should be implemented.