The raw datasets accompany manuscript titled " Vaccination of elms against Dutch elm disease – are the associated epiphytes and endophytes affected?", submitted by co-authors to Journal of Fungi. The data were collected to evaluate the potential impact of Dutch Trig ® vaccination treatment on two groups of associated biodiversity in elms ( Ulmus species), specifically, epiphytes (mainly lichens) and endophytic fungi, on two sites in Sweden, Stockholm and Gotland. The studies were conducted in spring term of 2022. Epiphyte coverage was assessed visually from four cardinal sites of 17 vaccinated (since 2011) and as many unvaccinated, healthy elms. Endophytic fungi were studied using a culture-dependent approach that results in cultures growing on agar plates. These isolates were assigned to morphotaxa groups (proxy for taxonomic groups) based on morphological traits. The growth rate of each isolate was assessed on a 3-step scale (low, medium or fast growth). ...