The aim of the present study was to characterise species of Antrodia s.l. from Patagonia, Argentina, and to determine their phylogenetic relationships by using morphological and cultural features as well as mating systems and ITS sequences. Phylogenetic trees generated from maximum-parsimony, neighbour-joining and Bayesian-inference analyses showed that the Argentinean collections were distributed inside the following three main clades: (1) ‘Antrodia clade’, with Antrodia ramentacea (Berk. & Broome) Donk as a sole representative; (2) ‘Amyloporia clade’, including Amyloporia nothofaginea Rajchenb. & Gorjón sp. nov. and A. stratosa (J.E.Wright & J.R.Deschamps) Rajchenb., Gorjón & Pildain comb. nov.; and (3) ‘Fibroporia clade’, with Fibroporia vaillantii (DC.) Parmasto and F. gossypium (Speg.) Parmasto. ‘Amyloporia’ and ‘Antrodia clades’ did not have strong molecular support; however, they were well defined with a polyphasic approach when other features such as the number of spore nuclei, mating systems and nuclear behaviour were added. Antrodia includes homothallic to bipolar species, with uni- or binucleate spores and normal nuclear behaviour. Amyloporia includes bipolar to tetrapolar species, with uninucleate spores and heterocytic nuclear behaviour. Fibroporia has strong molecular support and includes tetrapolar species, with uninucleate spores and normal nuclear behaviour. Amyloporia nothofaginea is described as a new species and two new combinations in Amyloporia are proposed. A key to the Antrodia s.l. species present in Patagonia is included.