At Shiratani, there is no torii, and there are no shimenawa and no shide. In Japan, forests are the spaces that most resemble European cathedrals, and there is a fundamental wrongness, an eeriness, about Shiratani’s lack, the kind of ghostliness one feels in a deconsecrated church. And yet one also observes, with every step, evidence of the human: The most popular (allegedly two-hour-long) path that cuts through the woods is a trail of scarred and rutted stones, slippery with moss so that your hands scrabble over wet tree roots for purchase, that was laid around 400 years ago, back when the forest was regularly plundered for timber to make shingles. It rains almost daily on Yakushima, and in the forest, everything is covered with a perpetual slick of dew or rain; one thinks of those early travelers, how they struggled up and down the hills in their straw sandals, cords of wood strapped to their backs.

But along with the aggressive tree-ness of Shiratani, it was what was missing that most reminded me of the forest of “Princess Mononoke.” Aside from the signs of the sacred, I realized, Shiratani also lacked flowers, and insects, and most unsettlingly, birdsong. You could stop and listen and hear only that plink of water that Miyazaki had recreated, but nothing else. You could look around you and see only green, green, green. Farther north, where the forest thinned, there were macaques, mean little creatures with flushed faces and disconcertingly human noses that walked on all fours as a bear cub might, but here, in its thickest section, there was nothing: The eye and ear searched and searched, but nothing was able to disrupt the dominance of the sugi themselves. It was as if the forest was so suffused with kami that there was no room for anything else.

The enchanted forest in “Mononoke” is similar, though with one big difference — that forest is the domain of the Forest Spirit, one of the most marvelous and frightening creatures invented in animation. By day, it is a massive, shaggy elk, its many horns blooming above its head like coral branches, its face resembling an ancient Japanese carved mask, with disquietingly human eyes. When it walks, wildflowers sprout, grow and die from wherever its cloven hoofs land; with a soft exhalation, it can kill or revive. But at nightfall, the Forest Spirit’s neck stretches toward the sky, and as the god grows, eventually looming above the treetops, it also becomes transparent, a kind of massive bipedal salamander, its back fringed with a frill of fins, stalking through the dark.

The Forest Spirit is, on one hand, simply more glorious evidence of Miyazaki’s fecund imagination. But his mysterious and discomfiting presence is proof as well of the director’s preoccupation with the symbols and mythologies (and values) of a prelapsarian Japan, particularly those associated with Shinto and Buddhist folklore. The spirit’s elk form, for example, is likely an allusion to the deer, considered in both Shintoism and Buddhism to be a messenger of the gods (and his nighttime form borrowed from a Shinto legend of a spirit who can create footsteps in a frozen lake). In “Totoro,” the two girls, caught in a storm, pass a stone statue of a Jizo, a bodhisattva responsible for protecting children and travelers. And in 2001’s “Spirited Away,” the story of a girl’s path to independence while being forced to work in a traditional Showa-era bathhouse frequented by gods and demons, and Miyazaki’s second masterwork, a river god purifies himself in a steaming tub of water, washing away the detritus of men. Many of Japan’s greatest directors — including Yasujiro Ozu and Akira Kurosawa, to name just two — wrestled, repeatedly, with whether and how industrialization had in some way fundamentally altered the country’s essential qualities: its worship of the natural world, its humility before it, its soul. But none have captured, in such color and with such verve, the profoundly pagan sense of twinned superstition and celebration that informs the culture, the way the country masquerades as a contemporary one in its surfaces and in its technology while still believing, unswervingly, in gods and monsters, in the divinity of a tree.