Tropical ecosystems harboring aphyllous vanillas are subjected to disturbances exposing vines to open habitat, drought, and forcing them to use smaller supports. Our aim is to study the responses of Malagasy aphyllous vanillas to changes in their environment with focus on the root system. Firstly, we compared the characteristics of roots in two habitats, one preserved with a close canopy and the other degraded with an open canopy. Secondly, we analyzed the variations in root anatomical traits along a North-South gradient characterized by decreasing rainfalls. The results showed that vines were more frequent and the number of roots lower in open compared to close habitat (35 against 42 adhesive roots per individual and 8.3 against 20.6 aerial roots per support tree). However, they have developed more filiform roots that behave like twists for anchoring stems to small size supports, in degraded habitat. Xylem vessel tapering of aerial root as they are distant from soil is interpreted as a strategy to improve water transport with height. Vanilla plants occurring in semiarid climate (Southern Madagascar) have larger roots with more vascular bundles than those in humid environment (Northern Madagascar), with the exception of those from Darainy, which have anatomical traits similar to those of southern vanillas. The adhesive roots showed particular morpho-anatomical characteristics that facilitate anchoring to supports of different sizes in order to maximize spatial colonization, while the aerial roots are mainly specialized in water and nutrient absorption.