The main aim of the present study was to characterize populations of invasive pathogens – causal agents of three major forest tree diseases: alder decline (Phytophthora alni species complex – in seven European countries with an emphasis on Lithuania and Switzerland), Dutch elm disease (DED, Ophiostoma novo-ulmi – in Lithuania) and ash dieback (Hymenoscyphus fraxineus – in Lithuania and Switzerland). Microorganism communities in environment of declining alder trees were investigated and compared in Lithuania and Switzerland. Microsatellite analysis of P. x alni and P. uniformis DNA samples from seven European countries revealed relatively high genotypic diversity of P. x alni populations, while in P. uniformis populations it was very low. As causal agent of DED, only O. novo-ulmi (and its intraspecific hybrids) was isolated from symptomatic elm trees in Lithuania. High genotypic diversity and high probability of intraspecific recombination were revealed within O. novo-ulmi populations. Microsatellite analysis of H. fraxineus DNA samples indicated high genotypic but low genetic diversity across Lithuanian populations of the pathogen. A significant correlation in virulence of the same set of H. fraxineus isolates was observed in two F. excelsior seedling inoculation experiments, indicating that such experiments provide reliable results for virulence assessment. It was also demonstrated that isolate virulence doesn’t correlate with its mycelium growth rate in vitro.