A new subspecies of Epipactis microphylla, proposed as subsp. cossyrensis is described and illustrated from Pantelleria, a volcanic island near Sicily. It differs from subsp. microphylla mainly in the shape and size of leaves and bracts and several floral traits. This taxon, previously attributed to E. pollinensis, a species currently treated as a synonym of E. purpurata, grows in the undergrowth of thermophilous woodlands occurring on the top of the island, where it numbers a few tens of individuals. The conservation status, phenology and taxonomic remarks are provided. Keys for the species belonging to the Epipactis atrorubens group (= subsect. Atrorubensae), including E. microphylla, are presented.