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A tree attaining, according to Shirasawa, a height of 90 feet in Japan, with a tapering stem, open in habit as cultivated in England, and not forming such a dense pyramid as Thuya plicata. Bark of the trunk scaling off in very narrow longitudinal papery strips. The bark commences to scale on young branches of less than a half inch in diameter. The branches curve upwards towards their extremities.

The branch-systems, 3–4 pinnate, are disposed in horizontal planes, which droop at their outer extremities. Primary axes terete, with leaves densely crowded, all the four sets ending in short, rigid, thick, free points, glands being absent. The leaves on the ultimate branchlets are obtuse, and not acutely pointed as in Thuya plicata; and glands may be present or absent on the flat leaves. The foliage is light green above, while on the under surface there are whitish streaks, somewhat triangular in outline, which exceed in area the greener parts.

Male flowers cylindrical, with 6 decussate pairs of stamens. The cones are deflected, ovoid, and composed of 5 to 6 pairs of scales, of which the second and third pairs are larger than the others and fertile. The scales are broadly oval, with a rounded apex, from below which externally is given off a short, broad, triangular process, projecting from the scale at right angles or nearly so. The seeds, three to each fertile scale, and nearly equal to it in length, differ considerably from those of Thuya plicata and Thuya occidentalis, the wing being narrow, not so scarious in texture, entire, and not notched at the summit.

Fortune discovered Thuya japonica in cultivation around Tokyo in 1860, and sent home seeds of it to the nursery of Mr. Standish at Ascot, who distributed plants under the name of Thujopsis Standishii. Maximowicz, who had also seen it cultivated at Tokyo, gave the species its first authoritative name in 1861. Maries found it growing wild on the mountains of Nikko, in central Japan, in 1877. Sargent, who, in company with James H. Veitch, met with a few solitary specimens on the shores of Lake Yumoto in these mountains, at 4000 feet altitude, describes it as a small pyramidal tree of 20 to 30 feet high, of open and graceful habit, with pale green foliage and bright red bark. Shirasawa, however, states that it attains a height of 90 feet, with a diameter of stem of nearly 6 feet; and that it grows in the central chain of Hondo, in the mountains of Kaga, Hida, and Shinano, at elevations of 2000 to 6600 feet. The stem, according to Shirasawa, is often twisted, and gives off great wide-spreading branches.