While most Pokemon are just technicolor merchandise fodder and some are literally just actual animals, there are a disturbing amount of them that are rooted in folklore and spiritual iconography.
Now, the thing about ancient legends and folk tales is that they weren't created with an ESRB rating in mind, so while these Pokemon are free to be sassy and adorable, their origins harken back to a much darker age. Some of these creatures would even make the Brothers Grimm say "yeesh, tone it down a little". Here's 14 pocket monsters based on actual ancient terrors that have survived through the ages.
Where did Game Freak get the idea for a magical version of Japan swarming with bizarre supernatural monsters? From Japan itself. The country's folklore is infested with "yokai", creepy crawly monsters that come in hundreds of sizes and shapes. One popular yokai story is of "Futakuchi-onna" or "the two-mouthed woman". Once upon a time, a miserly farmer was overjoyed with his new wife because she miraculously never needed to eat, saving him a bunch of money. However, as the weeks went on he noticed that his grain supplies were getting dangerously low. It wasn't until one horrifying night that he awoke to find his wife asleep, but a second mouth on the back of her head was voraciously devouring his food stores. Tendrils of hair continuosly fed the mouth more and more rice, eating him out of house and home. Mawile is absolutely a reference to this story, sporting a demure gaze and one nightmarish mullet.
One of the most bizarre supernatural encounters ever reported was 1955's "Hopkinsville Goblin case" in which a rural farmhouse was supposedly invaded by a pack of 3-foot-tall aliens. Naturally, since the alleged monsters chose to appear in Kentucky, they were PROMPTLY and REPEATEDLY shot on sight. According to "eyewitness" accounts, the playful yet menacing creatures had small atrophied legs and bright glowing eyes, bullets seemed to bounce off their bodies, and they moved with an erratic swaying motion. There's a small but rabid "cryptid" otaku subculture in Japan, so it's very likely that Sableye's unique physicality was inspired by these creatures.
Somewhere, deep in the muddy shores, a giant is constrained. A creature so powerful that even its struggles to escape cause deadly earthquakes. This is the story of Onamazu the giant catfish. During the Edo period, fisherman claimed that catfish became more active right before an earthquake, this semi-useless factoid evolved into an urban myth that major earthquakes were CAUSED by one giant catfish. Once a terrifying and apocalyptic figure, Onamazu has been adapted in modern times as the official mascot of Japan's Earthquake Early Warning System. Whiscash, the giant whiskered water/ground type, is explicitly said to cause earthquakes or tremors in all of its pokedex entries.
Fox-spirits appear often in eastern mythology. Cunning, manipulative, and able to change their form in order to fool mortals, the kitsune is a trickster in many stories. One bizarre aspect of their lore is how they grow an extra tail every 100 years. Once the number of tails grows to nine, they are said to gain infinite wisdom and godlike power, turning their red fur a golden white. That's why Vulpix evolves by gaining 3 tails and a change in fur color. I can't believe I got through this whole entry without mentioning Naruto- ah damn there it was.
In Japan, Jynx is understood to be a cheap shot at ganguro, a fashion trend that involves gaudy clothes, unusual amounts of makeup, and bleach blond hair. The most extreme practitioners of the look were labeled yamanba, a reference to the legend of Yama-uba. According to the stories, Yama-uba lives alone in the icy mountains and lures wayward travelers into her cabin to devour them. Jynx's unusual Ice/Psychic typing really only makes sense once you understand the "flesh devouring mountain witch" connection.
According to Chinese legend, the Yellow Emperor Huang Di was on patrol near the East Sea when he encountered Bai Ze, a magnificent beast with a flowing white mane, large horns, and several eyes. The monster taught the Emperor about the secrets of the supernatural world and how to defeat thousands of types of supernatural beings. The myth of this mysterious white creature spread to Japan as well in the form of the kutabe, which appeared before a village to successfully warn them of a coming plague. This definitely fits Absol's pokedex entries, which talk about its habit of emerging from the wilderness to inform humans of oncoming disasters. Take a look at the dark spot in the center of Absol's head and tell me that's not supposed to be where the third eye opens.