Macaronesia is an important biodiversity hotspot in the Mediterranean bioclimatic region, hosting a number of endemics, and encompassing outstanding refugia for ancient Tertiary plant lineages. We investigated past occurrence and present distribution of yew (Taxusbaccata L.) in the Madeiran archipelago, providing preliminary morphological and genetic descriptions and addressing conservation issues. Fifty-eight individuals presently occur in 19 micro-populations, as probable survivors of the continued yew exploitation across the centuries. Plants were characterized and compared with Euro-Mediterranean provenances by leaf morphology, anatomy, nuclear ITS (Internal Trascribed Spacer) and plastid trnS-trnQ DNA markers. The Madeiran provenance showed peculiar leaf size and morpho-anatomical characters. DNA sequences revealed a basal position of Madeiran yew in the Baccata phylogenetic clades along with the Azorean provenance. Gathered data suggest the survival of a lineage of T. baccata different from those on the continent, and with a possible closer derivation from the species' ancestors. Such evidences provide a base for identifying a great phylo-and phytogeographical interest of the Macaronesian provenance, and confirm the role of the archipelagos to preserve relict flora and lineages. The risk of extinction of Madeiran yew also calls for conservation strategies and restoration programs for a prompt species rescue.