In this work, we present a dataset, which provides information on the structural diversity of some endemic tropical species in Madagascar. The data were from CIRAD xylotheque (since 1937), and were also collected during various fieldworks (since 1964). The field notes and photographs were provided by French botanists; particularly by Francis Hallé. The dataset covers 250 plant species with anatomical, morphological, and architectural traits indexed from digitized wood slides and fieldwork documents. The digitized wood slides were constituted by the transverse, tangential, and radial sections with three optical magnifications. The main specific anatomical traits can be found within the digitized area. Information on morphological and architectural traits were indexed from digitized field drawings including notes and photographs).