This revision of Cantharellus in Madagascar deals with species that are associated with strictly endemic host trees and shrubs. Based on morphological differences and molecular sequence data of the tef-1 gene, five new species are proposed (C. albidolutescens, C. ambohitantelyensis, C. ibityensis, C. paucifurcatus and C. sebosus), as well as one new subspecies, C. subincarnatus ssp. rubrosalmoneus, whereas C. decolorans and C. platyphyllus ssp. bojeriensis are epitypified. A key is provided to all Cantharellus that grow with native vegetation in Madagascar.