Molecular results show that the genetic distances between and within Ixora margaretae dry and humid stands vary similarly. Accordingly, humid stands are interpreted as a part of the broad newly delimited I. margaretae, occurring in fragmented habitats. Morpho-anatomical data show that several features, such as the bark types, the individual height, and the fruit fleshiness result from genetic variability expressed under environmental constraints. However, other features are interpreted as acclimatisation of populations to local conditions, such as the convergent erected receptaculum pollinis for dry and humid stands, obtain by two different anatomical processes. All data suggest that I. margaretae is a species showing genetic isolation and relative adaptations to environments of populations in both humid and sclerophyll forests. This illustrates potential ongoing speciation processes for several populations in both forest types. A scenario showing the successive habitat modifications from humid to sclerophyll forests that can explain the persistence of the species in sclerophyll areas is proposed.