Members of the Phialocephala fortinii s.l. – Acephala applanata species complex (PAC) are ubiquitous endophytes forming complex communities in roots of conifers and ericaceous shrubs across the Northern hemisphere. Two kinds of disturbances (clear-cutting and drought) and their effects on the resident PAC community, as well as on the introduction of alien strain 7_45_5, were investigated using mesocosms with natural Norway spruce (Picea abies) regeneration, both under controlled climate chamber conditions and natural conditions in the forest. This is the first record of successful strain introduction into a well-established forest ecosystem. Introduction was more successful when planting inoculated living spruce saplings, compared to inoculation using autoclaved colonized roots. 7_45_5 was less assertive in the forest, where Phialocephala subalpina clearly dominated. Clear-cutting favored A. applanata and simultaneously reduced the overall frequency of PAC. Drought only had a significant influence on 7_45_5, which was more abundant in dry than moist, non-clear-cut plots. To conclude, disturbances and arrival of foreign strains can alter resident PAC communities significantly.