Phytophthora austrocedri was identified as the primary pathogen causing the "Mal del ciprés" disease in Patagonia, which affects the endemic conifer Austrocedrus chilensis. Trees present root necrosis that may extend to the stem. This study aimed to describe the histological alterations occurring during P. austrocedri infection of roots of A. chilensis seedlings. Plants were inoculated at the roots and histological studies were performed four weeks post-inoculation. Safranin-fast green, phloroglucinol-HCl, toluidine blue, lugol and diaminobenzidine stains were used to describe and compare anatomo-histological features observed in roots of non-inoculated versus inoculated seedlings. In healthy tissues, the presence of Phi thickenings in cortical cells is reported for the first time for A. chilensis. In inoculated roots, it was observed necrosis of the epidermis and of the cortical parenchyma, and alterations in parenchymal cells (loss of turgor and content, without starch, presence of phenolic compounds). Lignin content remained unaffected by the presence of P. austrocedri. The area occupied by Phi thickenings was smaller in P. austrocedri-colonized tissues, and these structures showed an accumulation of polyphenols, absent in healthy tissue. Parenchymal cells, tracheids, and rays, showed production of hydrogen peroxide. Results evidenced that A. chilensis triggers mechanisms to restrict the infection, but P. austrocedri manages to evade them.