Dark septate endophytic fungi (DSE) may have an important functional relationship with host plants, but these functions and the colonization process remain unknown. We made microscopic observations of the growth of an endophytic hyphomycete in Chinese cabbage roots to understand its colonization process. This hyphomycete was Heteroconium chaetospira, a suspected DSE. Three weeks post inoculation, some hyphae became irregularly lobed and formed microsclerotia within host epidermal cells of healthy plants. In stunted plants, hyphae formed closely packed masses of fungal cells within host epidermal cells, but conidiophores rarely broke through the cell walls to produce conidia.