Endophytic fungi associated with Pinus tabulaeformis Carr. were investigated in the Dongling Mountains of Beijing. A total of 16,200 tissue segments of P. tabulaeformis from four sample collections were processed, and 10,659 fungal isolates were recovered. The overall colonization and isolation rates of endophytic fungi from high to low were spring > winter > autumn > summer and in different tissues were bark > needle > xylem, irrespective of sampling seasons. The colonization rates of endophytic fungi of needles increased with age in the four sample collections. There were no significant differences of the colonization rates of endophytic fungi among 1-, 2-, and 3-year-old bark and xylem, except for significantly lower colonization rates in 1-year-old bark than in 2- and 3-year-old bark in summer. A similar trend of the isolation rates of endophytic fungi occurred. A total of 24 fungal taxa were recorded, of these five taxa Alternaria alternata, Leptostroma sp., Pestalotiopsis besseyi, Phoma lingam, and Phomopsis archeri, were consistently isolated as the common fungi in each sample collection. Our results suggest that some fungi show a certain degree of tissue recurrence or specificity, and the composition of endophytic assemblages is not conspicuously influenced by the seasonal factor.