Natural tree regeneration is a fundamental process in forest ecosystems ensuring the persistence and resilience of forest stands. Research on natural regeneration of European beech (Fagus sylvatica) in Central European forests has mainly focused on the impacts of abiotic processes, while little is known about the impact of pathogens. The aim of this study was to isolate Phytophthora species and identify the role that they may play in the decline of beech seedlings in Poland. A total of 1192 Phytophthora isolates were obtained from 300 symptomatic beech seedlings (60 seedlings from each of five stands): 638 isolates from seedlings exhibiting above‐ground symptoms and 554 isolates from seedlings that had roots with damping‐off symptoms. Based on morphological and molecular identification, the isolated species were Phytophthora cactorum, P. × cambivora, P. europaea, P. gonapodyides, P. plurivora and P. pseudosyringae. P. cactorum, P. × cambivora, P. europaea and P. plurivora were the most frequently isolated species from both above‐ and below‐ground organs. P. cactorum, P. × cambivora and P. plurivora were the most pathogenic species in the pathogenicity trials and caused 100% seedling mortality within 14 days of inoculation of the above‐ground organs. One single isolate of P. europaea was similarly pathogenic. P. gonapodyides, and P. pseudosyringae induced seedling mortality after inoculation of the cotyledons but not the roots. Our results demonstrate that Phytophthora may play an important role in reduction of naturally regenerated European beech seedlings.