Endophytic fungi are widespread in plants and affect the host fitness and population size. We found 12 fungal taxa in C. secalina, a critically endangered species in several European countries, at two study sites in Poland. The most frequently occurring fungal taxa were Colletotrichum destructivum and Acremonium sp. Both taxa were found in half of the examined tussocks. The highest number of fungal taxa was noted in the C. secalina plants growing in the roadside area, where 7 of the 12 identified fungal taxa occurred. These fungi, inhabiting leaf tissues, are known for their pathogenicity but no visible symptoms of any diseases were observed on C. secalina leaves. This suggests that these fungi are latent pathogens.