Saurel pike/Aji from Suruga Bay, Shizuoka Prefecture

Very few people will disagree with the notion that Japan is the ideal place to discover and savour sushi and sashimi in the whole world. Nevertheless, there are a few rules of the thumb to respect even in this gastronomic paradise.
The overriding rule is that you should try and eat only local fish or seafood.
Tsukiji might be considered a sushi paradise by Tokyoites, but the cheap prices enjoyed by tourists cannot conceal the reality: the fish and seafood are “imported” from all over Japan and beyond!
More than often, Edomae (Tokyo) sushi is nothing but a clever way to “dress up” ingredients to lure officionados (and customers) into believing they are eating top quality sushi (with the consequent prices).
Now, if you have the chance and time to explore Japan beyond Tokyo, you will discover an unfathomable treasure trove of gastronomic pleasure and knowledge!
After all, this country is a vast archipelago stretched across greatly different seas and climates, making for a diversity difficult to equal.
So, even if you cannot possibly explore all the shores of this nation, make a point to learn about the food available wherever you choose to stay.
The same goes for residents, not only for their own sake, but for that of their visitors and friends!

Sushi set with fish all caught in Suruga Bay, Shizuoka Prefecture

You also ought to do some homework. Sushi chefs worthy of their salt will be only too happy to answer questions to genuinely interested customers and come up with revelations of their own.
As an example to illustrate the need for some basic knowledge, in Hokkaido “oyakodon” is not cooked chicken and omelette on a bowl of rice, but raw salmon and its roe spread on top the same bowl of rice!
Likewise, the same fish will more than often be sold under a myriad of names.
Many morsels will not be found anywhere else as “sakura ebi/cherry shrimps” and fresh”shirasu/sardine whiting” in Shizuoka Prefecture.
Sashimi in most cases has to be perfectly fresh as typified by “kubiore saba” in Yakushima Island where fishermen break the neck (“kubiore”) of mackerels (“saba”) to preserve their quality upon catching. The same fish will be served within a few hours, or less, on the local tables.
On the other hand, tuna sashimi is best consumed after ripening for a few days in a refrigerator.
In Hokkaido, large shrimps, especially “botan ebi” will be served only raw, whereas “kuruma ebi” will be first boiled in other regions.

If you ask for “tataki”, make sure it means the whole fish, especially “aji/mackerel pike” that will be served finely cut as tartare atop the dressed fish.

Flying Fish/Tobiuo sashimi from Yakushima Island

On the other hand, sushi follows different rules.
Fish and seafood placed on “donburi” (bowl) are usually of the freshly brought variety but fish served as nigiri is prepared in a different way.
The greatest sushi (and this cannot be done in Tsukiji!) are made with fish which has been gutted and cleaned live within seconds, then dressed into strips/fillets left to mature in a refrigerator on clean cloth/kitchen paper. This can be done only with fish caught locally!
The same obviously goes with shellfish and other marine ceatures: One cannot sample better “uni/sea urchin” away from Hokkaido or sakura ebi from Shizuoka.

Vegan and vegetarians, upon finding a restaurant willing to satisfy their priorities should also ask for food grown locally, a search easier than one might think at first as there are many non-meat eaters in this mainly Budhist country.
The same vegetables will make for the perfect combination when associated with local fish!

RECOMMENDED RELATED WEBSITES

With a Glass,
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Adventures in Bento Making, American Bento, Beanbento, Bento No1, Bento Wo Tsukurimashou, Cooking Cute, Eula, Hapabento , Happy Bento, Jacki’s Bento Blog, Kitchen Cow, Leggo My Obento, Le Petit Journal Bento & CO (French), Lunch In A Box, My Bento Box, Vegan Lunch Box; Tokyo Tom Baker, Daily Food Porn/Osaka, Only Nature Food Porn, Happy Little Bento, The Herbed Kitchen, J-Mama’s Kitchen, Cook, Eat, Play, Repeat; Bento Lunch Blog (German); Adventures In Bento; Anna The Red’s Bento Factory; Cooking Cute; Timeless Gourmet; Bento Bug; Ideal Meal; Bentosaurus; Mr. Foodie (London/UK); Ohayo Bento

Must-see tasting websites:

-Sake: Tokyo Through The Drinking Glass, Tokyo Foodcast, Urban Sake, Sake World
-Wine: Palate To Pen, Warren Bobrow, Cellar Tours, Ancient Fire Wines Blog
-Beer: Good Beer & Country Boys, Another Pint, Please!
-Japanese Pottery to enjoy your favourite drinks: Yellin Yakimono Gallery