Japanese Marten is found in forests, and can occur in suburban areas with sufficient trees. It "plays a key role as a relatively long-distance seed disperser for major component species with large and flesh-rich fruits in the subalpine scrubland" (Otani 2002). It forages on a wide variety of fruits (Otani 2002) but is presumably predominantly carnivorous. Tatara (1994) used radio-telemetry to investigate Japanese Marten habitat selection, and showed that M. m. tsuensis preferred to forage and rest in deciduous and evergreen broad-leaved forests, and avoided coniferous plantations and open fields. For M. m. tsuensis forest edge was categorised as the most critical factor affecting home range size in relation to food and resting site availability. The race M. m. melampus was camera-trapped in the Akaya area at elevations ranging from 609-1,687 m asl, indicating no affect of elevation (Hoshino et al. 2013). On Japan the species prefers broadleaved forest as its primary habitat, suggesting that it relies on the complexity of the forest structure for cover and fruiting trees. Tatara (1994) found that on Tsushima martens avoided areas with young trees and trees of low stature and preferred areas with mature and taller trees.

Two subspecies of Japanese Marten have been described: M. m. melampus of Honshu, Shikoku, Kyushu and adjacent islands, and M. m. tsuensis of the Tsushima islands, which lie between Kyushu and the Korean Peninsula (Masuda 2009). It has been introduced on Sado Island and Hokkaido (Masuda 2009). It has been recorded in the southern Korean Peninsula but there are no locality details to prove a wild origin and no native population has been confirmed (Won and Smith 1999, Abe 2005). It has been found from sea level to 2,000 m asl.

Japanese Marten is present in protected areas. Commercial forestry should consider refinements to harvest practise that would allow a reduction in incidental habitat loss for this species (Tatara 1994). Conservation of deciduous forest is especially important (Nakamura et al. 2001). The population of the Tsushima Islands is protected as a Natural Monument in Japan.