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The two best fish markets in town are Mutual Fish, as everyone else notes, and University Seafood and Poultry off University Way NE in the U District. Hands down. I regularly shop at Metropolitan Market but after getting a not so good piece of fish, I said never again for seafood.
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Mutual Fish on South Rainier is my go-to place, even though it's out of the way. I do occasionally purchase fish from one of the mongers at Pike Place (both the throwers as well as the mongers located near all the produce stands), but only the throwers if I have a Groupon, and only the one near the produce stands if I'm already there for produce and have a specific fish in mind. And don't underestimate Uwajimaya or Seafood City - they both have surprisingly good stocks, and oftentimes (especially in the case of Seafood City) types of fish you can't find anywhere else in town.
If you live closer to Ballard, then I'd imagine Fisherman's Wharf.
If Cap Hill is more your haunt, Taylor Shellfish is well received.
