Bears: Japan is home to both the Asian black bear and the brown bear (Only in Hokkaido).Although bear encounters are rare, they can be dangerous if provoked. To minimize the risk, make noise while hiking, clap your hands, whistle, and store food securely. If you happen to encounter a bear, remain calm, back away slowly, and avoid direct eye contact. (There is no evidence that bear bells have any effect or reduce bear encounters, clapping is louder and less annoying)

Hornets: The Japanese giant hornet has a painful and long lasting sting. Though not inherently aggressive, disturbing their nests can provoke these hornets to defend their territory fiercely. Stay away from their nests, and if you encounter a hornet, move slowly and maintain a safe distance.

Boars: Wild Boards are a common inhabitant of Japanese mountains (especially around Kobe) While boars are typically shy, they can be aggressive if they feel threatened or have piglets. Keep your distance, and if you come across a boar, calmly back away and avoid any sudden movements. (When I did meet a mum with piglet, she was definitely not happy and followed us but didn't charge)

Monkeys: Japanese macaquesalso are also a common sight in some regions (Konoshidaira Campground in Kamikochi has a big group and I also always see them when hiking in the Toyama region). While most are accustomed to human presence, don't feed or interact with them. I've had a single male charge at me on Yakushima island after I surprised it coming around a corner fast. I was certain it was gonna bite me because it was so aggressive. I swung my backpack at it to keep it away. My scariest animal encounter.

Horseflies: During the warmer months, horseflies can be really bothersome. Protect yourself by wearing insect repellent and appropriate clothing to minimize bites. Japan has a red variety which looks a bit like a hornet and they are huge. They can be very aggressive and some areas have a lot of them.

Mountain Leeches: Rainy periods can bring out mountain leeches on forest floors and damp areas. Wearing leech socks and suitable footwear will help protect against bites. If you encounter a leech, use salt and it will come right off. Certain mountain ranges in Japan are invested with leeches and they will get you as soon as you stop walking. Worst I've seen was just outside of Nagoya in the Suzuka mountains.

Dangerous Snakes: Japan is home to  four venomous snakes that hikers should be cautious of. Among them, the Mamushi (Japanese pit viper) stands out.  While rare they can sometimes be encountered while hiking and I've seen two as well.  If your going through high grass be careful to not accidentally step on one. If you plan on hiking in Okinawa, be cautious of the Habu (also a pit viper). We were warned when doing the Iriomote Island Crossing to make sure to be out of the jungle before it gets dark, as they come out to hunt at night.

Japanese Serow: The Japanese serow is a goat-antelope species known for its remarkable climbing abilities. Kamoshika are not dangerous at all but very shy and rare, so if you do see one count yourself lucky and don't disturb it.