Healthy-looking needles were randomly collected from Pinus mugo ssp. uncinata at two sites in the montane zone with different edaphic and microclimatic conditions and examined for the diversity of endophytic fungi. One site is on a mountain ridge, the other in a peat bog. On average, about 35–40% of the needles were colonized at both sites. Eleven species of fungi were isolated. Cenangium ferruginosum and Cyclaneusma minus dominated the endophytic mycobiota of the tree stand along the mountain ridge. C. ferruginosum and Lophodermium pinastri were the dominant species in the needles of the trees in the peat bog. C. ferruginosum and L. pinastri occurred mainly in the needle tip; C. minus occurred most frequently in the middle segment of the needles. The needle base was rarely colonized by these fungi. Endophyte colonization of trees along the mountain ridge increased significantly from the uppermost trees to the ones further down the ridge. No clear pattern of colonization was observed for trees in the peat bog except for the colonisation by L. pinastri, which showed a tendency to form infection centres. Species composition was constant within sites, but the frequency of colonization by C. minus and L. pinastri varied greatly among trees.