Hidden in Harajuku sits this unassuming humble home with a shabby-chic garden. The juxtaposition itself feels thoroughly Japanese, even before the fresh seasonal dishes arrive at rustic tables indoors and on the cozy outdoor terrace. Owner Yuri Nomura is known as the Alice Waters of Japan for her tireless promotion of organic living and dining. The day’s well-priced omakase menu items are served on large sharing plates; the English-speaking manager happily translating for foreigners who find there way to this leafy haven.

This hard-to-find cocktail bar is the sort of place that makes Tokyo’s nightlife scene exciting and full of surprises. Gen Yamamoto is a Tokyoite who spent eight years training in New York’s cocktail scene before returning home to open his eponymous bar. Tucked on a side street in a quiet neighborhood, Gen Yamamato features only eight seats around a beautiful wooden counter. Gen, mixologist, maître d’ and bar manager all at once, never leaves his spot behind the bar, crafting cocktails for patrons who reverently sip their drinks while watching him mash, mix, microwave and create the innovative cocktails for which he is becoming famous. The menu is short and changes seasonally; in the winter for instance, drinks include quince, fennel and kumquat mixed with a variety of sochus and sakes. Go for a flight to fully appreciate the artistry behind each cocktail.

Gourmets agree that this is one of the very best places in Tokyo to sample sushi, which means it’s among the finest on Earth. This family-run restaurant has a decades-long history; the owner, Yosuke Imada, learned to make sushi from his father, who started the restaurant in 1936. Sushi connoisseurs speak the word “Kyubey” almost reverentially; reservations are essential.

Chef Yoshihiro Narisawa took the top honors when San Pellegrino launched an all-Asia 50 Best List in 2013 (having already racked up two Michelin stars). His minimalist-sleek dining room is unusually easy to find, among the car dealerships near Aoyama Itchome Station. Chef Narisawa earns raves as much for the aesthetics as the flavors of his dishes, each one intended to reflect a harmony with nature. In fact, he is known for serving surprisingly delectable (and distilled) soil, charcoal and bark, though his mains are creative takes on more conventional fare, such as a seas bass with cabbage and asari clams cooked in a paper bag. Narisawa also earns praise for the relative value of his nature-to-plate set menus.

This cavernous eatery is housed in a former bathhouse and has zero ambience. But gourmands head here to dig into heaping plates of tonkatsu, a heavily breaded and deep fried pork cutlet, topped with thick and tangy sauce and served with shredded cabbage and an earthy miso soup. This quintessentially Japanese dish was inspired by European cuisine in the late 1800s.

Note that the Japanese menu is a tome compared to the slender English menu, so be sure to peruse the former's pictures for more choices. You can also order the tonkatsu set menus, for a reasonably priced taste of Tokyo that really is finger licking good. While this restaurant, nestled among the snaking lanes of Harajuku, used to be very challenging to find, there are now signs like breadcrumbs leading newcomers off the main avenue, Omotosando and straight to Maisen’s front door.

For kaiseki and kappo ryori, head to Nihonbashi Yukari. Come for lunch if you are on a budget, but a dinner is also great. For lunch, you can reserve a special bento ahead of time or order one of the daily specials. There are private tatami rooms in the basement, but the coveted seats are at the counter where you can watch the chef's artistry first-hand. Beverages include a nice selection of Japanese wine and an original beer that chef Nonaga created to specifically pair with Japanese food. The dynamic chef is passionate about Japanese cuisine and sharing it with those who are curious.

Tokyo’s current three-Michelin star darling, chef Seiji Yamamoto, has been cited for his “defiant perfectionism” and called “a brilliant experimentalist” by the world’s toughest critics. Diners often sit silently in the glam, gold-on-black dining room, their attention and senses consumed by Yamamoto’s intense modern Japanese cuisine, made with Japanese-only ingredients, a self imposed edict he religiously observes.

Japanese attention to detail and the nuances of haute French cuisine blend seamlessly under Chef Shuzo Kishida, who trained in some top French restaurants in Japan for seven years before joining Pascal Barbot’s L’Astrance in Paris in 2003. When he returned home to open Quintessence in 2006, the restaurant immediately earned a whopping three Michelin stars. Kishida’s modern French kitchen incorporates Japan’s extraordinary produce to turn out dishes like sea urchins with leek, croutons and organic vegetables. Diners should come with an open mind and palate since lunch and dinner are menu carte blanche based on fresh seasonal products and change daily, but always involve Kishida’s signature cuisson (low-temperature long-time roasting). In typically meticulous Japanese fashion, the restaurant makes note of what you ate, thus you will never be served the same meal twice.

Established in 1885, this humble, ten-seat eatery in Nihonbashi is still helmed by descendants of founder Mosaburo Okuda. These days, two generations of tempura masters stand behind the wooden counter, coating fresh prawns, unagi and unexpected items like persimmon leaf in tempura batter, which originally came to Japan with 16th century Portuguese seafarers.

In the shadows of the city’s landmark Tokyo Tower is one of the most unique dining experiences in the city. Tofuya Ukai specializes in tofu and soy products, but also serves seafood and meat. The menu is kaiseki style with several courses. There are over 55 private rooms and over 500 seats, but you feel like you are the only diners. Each party gets its own private room that overlooks a Japanese garden.

Yoshitake may be small on space—there are only six seats—but what it lacks in size it more than makes up for in flavor. The three-Michelin-starred sushi bar respects the traditional principles of the cuisine, presenting simple ingredients in beautiful arrangements. Hidden away on the third floor of what looks like an office building, Yoshitake may be hard to find, but the impeccable offerings and intimate atmosphere make it worth the hunt. Reservations should be made at least one month out.