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I live in Hakodate, a medium sized city in the south-western corner of Hokkaido. It is a port city with tourism and seafood as its main industries. There isn't much else in Oshima (the name of the peninsula); mountains, forests, some farmland and a scattering of small fishing villages. The area is volcanically active meaning there lots of hot springs. The Tsugaru Straits separate Hokkaido from the main island of Honshu.
In terms of birding it's a pretty overlooked area. The most famous places for birds in Hokkaido are all far away to the east: Kushiro, Nemuro and Rausu. Oshima lacks 2 of the island's star birds, the Japanese Crane and Blakistons Fish Owl, but many other Hokkaido specialties are here such as Stellers Sea Eagle, White Tailed Eagle and Black Woodpecker. The 3 primary birding places are Hakodate itself, Lake Onuma and the surrounding forests plus the Yurappu Valley in and around Yakumo.
Other place I go birding in include the Oshamanbe area and the nearby Shizukari wetlands, Shikabe and Sawara, Menagawa, Kikonai and Asabu.
Adult Stellers Sea Eagle in midwinter at Yakumo.
Black Woodpecker in early spring at Onuma.
Common Crossbill in late winter in Hakodate.
Long Tailed Duck in winter at Oshamanbe.
Japanese Green Pigeon in summer at Shikabe.
Red Necked Stint in autumn near Hakodate.
Harlequin Duck in early winter in Hakodate.
Brent Geese in Hakodate in early spring.
Varied Tit at Onuma in late winter.
Siberian Stonechat near Hakodate in early summer.
When to visit: Hakodate is good for birding in most months except high summer. Due to its location as the nearest point of Hokkaido to Honshu the migration season is generally excellent. Early to mid May and mid October are the best times. Shorebird migration is at its peak in early September. Oriental Honey Buzzard migration can be observed at Matsumae in late September. Huge numbers of Red Necked Pharalope and Short Tailed Shearwater pass through the Tsugaru Straits in May.
Winter is a good time across the region with many birds on the coasts and a good chance of seeing wandering winter passerines. The eagles are at Yakumo from mid November until early March, January is the peak month when they are both numerous and approachable.
Onuma is best in late spring/early summer before the forest growth gets too dense. Wildfowl and other waterbirds such as Grebes and Divers congregate in the many small fishing ports on the eastern side of the peninsula in mid to late winter.
Access: There are several daily flights to Hakodate Airport from Tokyo as well as one each from Osaka and Nagoya. There are also a limited number of international flightsfrom other east Asian countries such as Taiwan. Hakodate is also connected to various small airports around Hokkaido. There are JR trains to the main regional hub of Sapporo and both train and ferry connections to Aomori in the north of Honshu. Both Onuma and Yakumo are on the Hakodate-Sapporo JR line. From late 2015 Hakodate is now accessible by bullet train from Tokyo.
Getting around: Hiring a car is essential if you do any birding outside Hakodate. Onuma is possible to visit by public transport as is the river mouth at Yakumo but buses are few and far between.
Place to stay: Hakodate has numerous hotels in all price ranges. In Onuma the most famous hotel is the Onuma Prince Hotel and there are several smaller hotels and guesthouses dotted around. Yakumo has more limited options: the hot spring hotel Obokoso is an option here, there is also a business hotel near the station.