The aetiology and frequency of Phytophthora spp. in discoloured xylem tissue beneath phloem lesions was investigated in a range of broadleaved trees infected with P. ramorum, P. kernoviae, P. cambivora, P. citricola and other species. Isolation was attempted from the inner surface of 81 sterilized discoloured wood panels (6 × 4 cm) from 53 trees. Discolouration mostly extended 1–5 mm into the xylem (75%), but incursions of 6–10 mm (10%) and 10–25 mm (15%) were frequent. Of the wood panels, 81% yielded Phytophthora spp. In 66 cases, both a wood panel and an overlying phloem panel were sampled. In 56% of these, a Phytophthora sp. was isolated from both the wood and the phloem panel. In 23% the Phytophthora sp. was isolated from the wood panel only and in 8% from the phloem panel only. Small ‘island’ phloem lesions, often in linear arrays adjacent to main lesions, were a common feature of Fagus sylvatica and Quercus spp. trees infected with P. ramorum or P. kernoviae. Island lesions were often connected by underlying strips or intermittent pits of discoloured xylem in line with the wood grain. Phytophthora ramorum, P. kernoviae and other Phytophthora spp. were successfully isolated from these connecting xylem features with P. ramorum and P. kernoviae also recovered from discoloured tissue 5–25 mm below exposed xylem surfaces 24–27 months after the overlying phloem was removed. These results show that these pathogens commonly occupy xylem beneath phloem lesions; that they can perennate in xylem tissue; that they can spread in xylem tissue ahead of phloem lesions; and indicate that they may initiate new phloem lesions in this way. Such colonization must lead to at least local xylem dysfunction. It is recommended that, if xylem discoloration is present, isolation of the Phytophthora sp. should be attempted from the xylem as well as the bark; also, that removal of infected outer sapwood should be undertaken during excision of bleeding lesions for disease control and in protocols aimed at preventing national or international spread of these tree stem pathogens.