Methane (CH₄) and nitrous oxide (N₂O) are important greenhouse gases. Generally, temperate forest soil is a sink of CH₄ and a source of N₂O. Japanese cedar (cedar) and Japanese cypress (cypress) are major species that were intensively planted in Japan after World War II. The major forest soils in Japan are brown forest soils (Gleyic, Dystric Cambisols) and black soils (Andisol or Fluvisol). To estimate CH₄ uptake and N₂O emission from forest soils and to clarify the effects of forest management on these gas dynamics, it is necessary to characterize the relationship between these gas fluxes and the site environment. We measured CH₄ and N₂O fluxes by a closed chamber technique at 26 sites from northern to southern Japan over 2 years. Soil type was classified as brown forest soils at 13 sites, black soils at 9 sites, and others (Gleyic, Haplic Alisols, or Acrisol) at 4 sites. The dominant vegetation was cedar at 8 sites, cypress at 6 sites, other conifers at 5 sites, and broadleaved trees at 7 sites. The annual mean temperature (6.0–22.7 °C), precipitation (1177–4957 mm), and elevation (55–1600 m) varied widely among the sites. The porosity, total carbon, and total nitrogen of black soil were larger than those of brown forest soil, indicating that black soils tend to be aerobic and to be rich in organic nutrients. Soil moisture, NH₄⁺ concentration, and nitrification ratio in cedar soils were higher than those in cypress soils, indicating that cypress soils are wetter and have relatively higher nitrification activity. The mean CH₄ uptake and N₂O emission rates at the sites were estimated to be 1.58 (0.07–4.2) mg CH₄-C m^-2 d^-1 and 1.88 (0.17–12.5) µg N₂O-N m^-2 h^-1. The CH₄ uptake rates were relatively higher than those previously reported (0.27–1.04 mg CH₄-C m^-2 d^-1) in Europe and the USA. On the other hand, the N₂O emission rates were lower than those previously reported (0.23–252 µg N₂O-N m^-2 h^-1) for temperate forests. Significant differences in CH₄ uptake were found among soil types (p < 0.05). Rates of CH₄ uptake by each soil type (mg CH₄-C m^-2 d^-1) followed the order black soil (2.3 ± 0.94) > brown forest soil (1.4 ± 0.66) > others (0.50 ± 0.57). Significant differences in the N₂O emission rates were found among vegetation types (p < 0.05). Rates of N₂O emission by each vegetation type (µg N₂O-N m^-2 h^-1) followed the order cedar (4.0 ± 2.3) > cypress (2.6 ± 3.4) > broadleaved (0.8 ± 2.2) > other conifers (0.7 ± 1.4). The CH₄ uptake rate was positively correlated with total nitrogen (r = 0.42) and total carbon (r = 0.48), and negatively correlated with bulk density (r = –0.54). CH₄ oxidation in the soil is regulated by aerobic microbial processes, which is to say that CH₄ oxidizers need CH₄, oxygen, and nitrogen to grow. We consider that atmospheric CH₄ and oxygen moves easily into black soil from the atmosphere owing to the high porosity of the soil. This explains the larger CH₄ uptake rate in the black soil. The N₂O emission was positively correlated with NH₄⁺ concentration (r = 0.45) and nitrification ratio (r = 0.43). We suggest that N₂O was produced by nitrification. Some reports showed a high nitrification rate in cedar forests. This could explain the larger N₂O emission observed in the cedar forests. Thus, the results suggest that soil properties of organic and inorganic nutrients in the surface soil affected CH₄ uptake, and that vegetation type affects N₂O emission from forest soils in Japan.