Mt. Hayachine in Iwate prefecture is characterized by serpentine site, which is known to have high concentrations of Ni. In general, few plants that can tolerate high concentrations of Ni can grow in serpentine soil. Thujopsis dolabrata var. hondai occurs naturally on Mt. Hayachine. In this study, we hypothesized that T. dolabrata var. hondai shows Ni tolerance due to detoxification by phenolics. We collected T. dolabrata var. hondai seedlings and root-zone soil from the Kadoma National Forest on Mt. Hayachine to analyze the concentrations of Ni, other heavy metals, and macronutrients. The seedling roots had high concentrations of Ni. Further, we conducted a pot experiment by using 1-month-old sterile seedlings grown in three types of sterilized soils-Kadoma soil (obtained from the Kadoma National Forest), Tsugaru forest soil, and nursery soil-and compared the concentrations of Ni, nutrients, and catechin, as well as the growth of seedlings in the different soils. The pot experiment indicated that the roots of seedlings grown in Kadoma forest soil contained high concentrations of Ni and catechin, which could act as an antioxidant and a possible Ni-chelating compound that detoxified Ni in the plant cells. We concluded that T. dolabrata var. hondai seedlings growing in the serpentine site of Mt. Hayachine accumulated Ni and could detoxify it by producing high concentrations of catechin.