Wakkanai is known for its variety of seafood. Catching and selling sea-dwelling creatures fish, crab, octopus, et cetera and drying of seaweed may be considered the industry in Wakkanai. Some of the best restaurants are the local ones located around Minami-Wakkanai station. If its all just too much to cope with there is a McDonalds to rescue you from starvation.
Bukkakedon
Serves nice bowls dons of seafood and rice as well as soups and some packed lunches you can take on trips. No, the name is not a joke, it actually just means pouring something over something
Densuke
Nice place dishing up homey seafood, quirky decoration with wooden figures and Buddha watching over you so you don't choke on the fish bones.
Harunaie
Soba shack with handmade noodles that brands itself as the northernmost soba shop in Japan, has its own organic farm for growing the buckwheat. Tasty!
Irohanihoheto
Part of a national chain, but it's actually quite nice, and the menu has pictures of nearly all the items. A good place if you are fed up with seafood. Western fare with a Japanese twist.
Masujo
Good beef tongue sets is the specialty, try the charcoaled ones, or you could go for the liver? Also has a good selection of spirits to kill your own.
Rupon
Another place near Minami-Wakkanai station. Small, cozy Izakaya style eatery, with a long desk to eat at and lots of wood everywhere. Freshly caught seafood from local fishermen. Try the sea urchin tofu "Hot-pot" or the miso marinated squid.
Tongarashi
Has a nice poster outside with pictures of the dishes if the Kanji's are daunting. Mainly seafood but not exclusively.
Kamui
Some nice casseroles and pots here with both seafood and meat, as well as a la carte fish and beef.