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Japan consists of a group of islands located between 45° and 32° north off the east coast of Asia. The main islands of Japan are Honshu in the center, Hokkaido in the north and Shikoku and Kyushu in the south. Basically all islands are described as relatively mountainous. Especially on Honshu you can find high mountains, including Mount Fuji (3,776 meters). The highest peaks on Honshu are often covered with snow all year round, and the same applies to the peaks on Hokkaido. This is also where Japan's famous winter sports regions are located.
Since Japan is basically separated from the Asian mainland by a narrow strip of sea, the sea plays a major role in the climate on the islands. Compared to other countries on the longitude, it is a bit milder in winter and precipitation levels are a bit higher. But still you have to keep in mind that Japan has cool and quite severe winters depending on the region - not only at the high altitudes. And basically you can find pretty much all climatic conditions in Japan. Extremes are, for example, the cold and snowy Hokkaido and the warm subtropical region of Okinawa. To make matters worse, Japan is basically located on a fault zone of several tectonic plates. This makes the country very susceptible to earthquakes. There are over 200 volcanoes in the country, about 40 of which are said to be active. Japan is actually shaken by earthquakes on a daily basis. Most are small, but some lead to severe environmental disasters.
Japan is usually divided into six climatic regions:
In winter there is heavy rainfall especially on the west coast of North Honshu and on Hokkaido. And here you also have good snowfalls and very cold periods in winter. These regions are usually reached by cold winter winds from Siberia. These warm up over the sea, but they also take up a lot of moisture and then reach the islands as very humid and still cool air currents. Here one has then in the winter high amounts of precipitation (see climate tables of Hakodate/Hokkaido and Akita/Honshu).
The south of Honshu, on the other hand, has relatively mild winters normally. Winters are also normally mild on the southern islands of Kyushu and Shikoku. Nevertheless, one must always be prepared for quite changeable conditions in winter. Mild and with little snowfall or frost the winters are at the coastal areas between the islands expect (see climate tables of Nagasaki and Ashizuri)
A lot of precipitation reaches Japan with the Bai-U in early summer and typhoons in late summer. Then it can rain heavily in central Japan and the south, for example. However, June and July are also quite notorious for heavy snowfall. Summers in northern Japan are normally relatively short, but quite warm. On the east coast there is more precipitation in summer than in winter. In the south and in central Japan the summers are usually quite warm and unfortunately often very humid, because here the air carries a lot of moisture from the sea. This is often very noticeable, especially in the larger cities. Typical for the climatic conditions of big cities at low altitudes is the climate table of Tokyo at the coast of Honshu.
The mountains have to be considered separately. Here the old wisdom applies - the higher, the cooler. This can lead to very good climatic conditions, especially in spring and summer. Then it is often quite sunny, but not very humid. In winter, on the other hand, the high altitudes are usually cold and quite snowy. The climate table of Oiwake at an altitude of just over 1,000 meters can provide some insight here.
A basic rule for Japan is that in summer, the south gets more sun than, say, the north of Honshu or Hokkaido. Also, it is normally said that spring is sunnier overall than summer. Conditions are then more pleasant overall - it is warm and sunny, but also dry and fresher or less humid. This is why spring is often referred to as an optimal time to travel to Japan.
In conclusion, the best time to travel to Japan is difficult to determine across the board. As mentioned, spring is not infrequently referred to as the best time to travel to Japan. This is undoubtedly true. You just have to be careful not to get into the range of the first rains of early summer and you also have to expect cooler periods (e.g. in the north/northeast). In addition, autumn with September and October is always mentioned as a good time to travel. But in recent years, Japan has been a reliable target for typhoons in September and in some places in October. Regarding typhoons, one must also be cautious about traveling in July and August (at least based on the experiences of the last few years). The summers are not to be recommended anyway. Depending on the region, they can be extremely humid and sticky. Summer, on the other hand, is interesting at higher elevations and in some coastal areas. For winter sports enthusiasts, the period from December to March can be interesting at the high altitudes of Honshu and Hokkaido.