AbstractAimIndian and Malagasy tropical rainforests share a common history that dates back to the fragmentation of Gondwana. We partitioned phylogenetic diversity across historical periods to uncover how such continental displacement led to the divergence of lineages, through vicariance and/or independent migration from other regions, influencing extant phylogenetic composition.LocationMadagascar and South India (Western Ghats).TaxonWoody vascular plants (tracheophytes).MethodsUsing a time‐calibrated megaphylogeny, we partitioned the phylogenetic diversity of Indian and Malagasy tropical rainforest assemblages, across evolutionary periods defined based on milestone events in these regions of geological history. We decomposed the relative proportion of lineages with extant representatives in each area as well as in both areas, to quantify the common and separate biogeographical legacies in the two regions. We identified an excess or deficit of shared and unique lineages for each period and region.ResultsThe proportion of shared lineages between Madagascar and India progressively decreased following the successive breakoff and isolation of Madagascar from the Indian‐Malagasy plate. Lineages unique to India are more numerous than expected at random in more recent time periods, whereas, lineages unique to Madagascar were significantly more present in older time periods.Main conclusionsThe flora of Madagascar harbours a greater number of ancient lineages than does the Western Ghats, consistent with the higher number of endemic families and genera of trees in Madagascar. More recent diversification in India could be related to the collision of India with Eurasia, which enabled subsequent biological interchanges.