From futuristic skyscrapers to centuries-old ateliers, Tokyo embraces the new while respecting its ancient traditions. It is also a city that is easy to navigate, as our resident correspondent reveals in her insider guide to the city's most enchanting sights, shops and neighbourhoods

The city's Aoyama area is home to the flagship stores of luxury brands

The city's Aoyama area is home to the flagship stores of luxury brands

Finely crafted kitchen wares at Nihonbashi Kiya in Coredo 1

Finely crafted kitchen wares at Nihonbashi Kiya in Coredo 1

Among Tokyo's greatest charms is its ability to embrace the past while leaping headfirst into the future – as reflected in the tiny shrines and old rice-cracker shops hidden in the shadows of 21st-century skyscrapers. Despite its epic population (it topped 37 million including the greater metropolitan area at the last count), the city also thrives on functioning smoothly: it is clean and punctual, with an easy-to-use public transport system and virtually no litter or street crime. Perhaps best of all is the adventure to be had in discovering Tokyo's sprawling urban patchwork of neighbourhoods, each as distinct in identity as they are entertaining to explore – from the shiny new design shops selling artisanal products in the Nihonbashi area to edgy lifestyle emporiums lining leafy riverside lanes in Nakameguro.

For many visitors, the day begins at dawn – be it due to the city's thriving nightlife or simply the jet lag. Either way, there are few better places to take in the daily sunrise show than Nihonbashi's Mandarin Oriental, Tokyo, more than 30 storeys above ground, from within the comfy confines of a king-sized bed in an east-facing guest room – complete with luxurious Egyptian linens, a pillow menu and a wall of windows framing expansive views across the city, including Japan's tallest building, Tokyo Skytree.

Occupying the top nine floors of a gleaming, 38-storey, César Pelli-designed tower, the hotel, one of the city's foremost luxury establishments, celebrates its 10th birthday in 2015. Inspired by the organic form of a tree, its look is unique, fusing natural materials – wood, stone and water – with a sleek, contemporary interpretation of modern Japanese design. The rooms bare testimony to this: rich, natural textiles, by Japanese designer Reiko Sudo, complement moon-like paper lanterns, leaf-motif bedding and bamboo.

Yanaka today offers a glimpse of an earlier, more tranquil Tokyo: quiet leafy lanes, low-rise wooden houses and leisurely cycling

The setting is equally memorable. Nihonbashi may be a thriving economic and commercial district of skyscrapers, office buildings and retail developments, but it is also one of the most historic areas in the city. It was here that the seeds of modern-day Tokyo were planted, thanks to the creation of a major commercial hub by a fast-growing community of merchants in the 17th-century Edo era. A peek just beyond the threshold of Mandarin Oriental, Tokyo will reveal instant traces of the city's ancient roots amid the fast-paced modernity.

A good place to start (after buying a delicious pastry from the ground-floor Gourmet Shop by Mandarin Oriental, Tokyo) is the Coredo Muromachi retail and food complex near the hotel. These three intimately designed new buildings, called Coredo 1, 2 and 3, combine contemporary Japanese minimalism with hints of Edo architecture. They have newly-built low-rise wooden façades, overhanging eaves, clean-lined rows of lanterns with traditional motifs, and fabric curtains marking streetside entrances to generations-old family businesses.

Tranquil, leafy lanes in the Yanaka area

Tranquil, leafy lanes in the Yanaka area

The futuristic Issey Miyake store in Omotesando

The futuristic Issey Miyake store in Omotesando

Find one of the best examples of high-quality local craftsmanship in Coredo 1 – Nihonbashi Kiya is famed in Japan, since 1792, for its exquisitely-made knives and kitchen utensils. Opposite is Hakuza Nihonbashi, another business dating back centuries, which specialises in all things gold – from handcrafted gold-leaf curtains, bags and jewellery to prettily-packaged jars of edible gold for sprinkling on food and cocktails. Nearby is Okui Kaiseido, devoted to the most unusual of possible holiday souvenirs, but found in any Japanese kitchen: dried kelp seaweed (konbu). The shop sells an array of specialist konbu and other condiments in rainbow-bright, handmade washi rice paper boxes.

A string of design hotspots in the new Coredo 3 space are also worth visiting, from the Kengo Kuma-designed soy-sauce store, Kayanoya (worth a look for the wooden barrel-inspired decor), to contemporary artisanal wares in Claska Gallery & Shop 'Do'.

Back outside, mere seconds away at the end of a stone street lined with Edo-style lanterns, is Fukutoku Jinja, a recently renovated Shinto shrine dating back to the 9th century that contrasts serenely with the surrounding modern towers. Stop by to wash your hands, toss a coin, ring a bell and make a wish, as is customary at local shrines, before picking a paper fortune omikuji from a wooden box by the entrance (ask the shrine staff to reveal the outcome, as they are written in Japanese; then tie to a nearby rope to bring good fortune or avert bad luck).

Shinto shrine Fukutoku Jinja in Nihonbashi

Shinto shrine Fukutoku Jinja in Nihonbashi

Venture further east to the Yanaka district to sample a taste of slow, local life, a rarity in a city that doesn't seem to stop. A hidden gem, Yanaka survived the wrath of World War Two bombings and successive natural disasters, unlike vast swathes of the capital that have been rebuilt several times over the centuries. As a result, Yanaka today offers a glimpse of an earlier, more tranquil Tokyo: quiet leafy lanes, willow trees, low-rise wooden houses, leisurely cycling, and old, family-run sembei rice-cracker shops.

Yanaka is also emerging as a mecca for a new generation of creatives, with a growing number of small design studios and craft ateliers setting up shop. One of the artisans is Hajime Sonoda, the name behind Sonomitsu, a bespoke shoe label that is acquiring increasing renown for its handmade, vintage-look leather designs. 'Yanaka used to be a residential area, attracting cultural people such as writers,' Sonoda explains from his atelier and boutique on a small and pretty tree-lined street. 'Today, it's still popular among creators. It's very peaceful, too, with old terraced houses, many of which have been turned into handicraft shops and food stores. The common virtue among residents is the desire to renovate old things rather than destroy them. So, unusually, people can experience a rural atmosphere here, even though it is part of Tokyo.'

One cult Yanaka outpost is Tokyobike, famed for its hip, light and minimal urban bicycle frames in a rainbow of colours. The company may have opened stores around the world in recent years, from Sydney to London, but it's still worth a trip to the Yanaka headquarters, set in a former liquor store built in the Thirties. The stylish bikes can be rented for the day, perfect for exploring the neighbourhood.

Other highlights include Scai the Bathhouse (an art gallery in converted public baths), whose diminutive size belies its status as one of Tokyo's best independent art spaces, representing high-profile artists such as Kohei Nawa, Lee Ufan and Anish Kapoor; and lunch at the atmospheric soba restaurant, Takajo (a favourite among local creatives, including Sonoda), where shoes are slipped off and rustic buckwheat noodles are served with delicious nihonshu (sake).

Soy-sauce store Kayanoya in Coredo 3

Soy-sauce store Kayanoya in Coredo 3

Classico is another go-to for contemporary design. Resembling a private residence, it's filled with lifestyle wares – from clothes and antiques to stationery and ceramics – many of which are produced by local artisans. Nearby is Yanaka Cemetery, where cherry trees burst into an explosion of pink blooms in the spring, and the Asakura Museum of Sculpture, whose Japanese rock and water garden is still perfection.

Tokyo's creativity is not confined to the slow life in Yanaka, however. The heart of Tokyo fashion can be found on the opposite side of the city in the Omotesando area, not far from the trend-triggering street fashion of Harajuku. Head here for the 'starchitect'-designed flagship stores of directional labels, as reflected in one stretch of the Omotesando boulevard, which is crammed with household names such as Issey Miyake, Comme des Garçons and Yohji Yamamoto.

Asakura Museum of Sculpture in Yanaka

Asakura Museum of Sculpture in Yanaka

Despite its bustling location, there are countless smaller boutiques to explore on the winding backstreets, which at times feel almost rural – as Noritaka Tatehana, the avant-garde shoe designer behind Lady Gaga's infamous heel-less heels, happily testifies. 'Tokyo may be the absolute metropolis, but this area has a strong sense of nature and spirituality,' Tatehana says from his studio, which has long been based here. 'It's central to Tokyo's fashion scene and it's here that the biggest trends are often seen ahead of New York and London.'

For a cup of coffee with a Japanese Zen twist, head to the much-loved Omotesando Koffee, a tiny wooden house on a quiet lane away from the crowds. Then continue walking through Omotesando towards Aoyama, past a string of designer headquarters, including the Prada store with its 'bubble-wrap' glass façade.

Around the corner is an old apartment block where a row of Arts & Science boutiques have opened, purveying clothes, shoes and lifestyle goods that fuse heritage craftsmanship with clean-lined modern design. Have a cup of tea and slice of cake at the equally stylish Down the Stairs café below, where locals gather at a large, central wooden table.

Nezu Museum in Omotesando

Nezu Museum in Omotesando

Opposite is the Nezu Museum, home to historical Japanese artefacts, from tea-ceremony tools to kimonos, not to mention a stylish minimalist makeover by acclaimed architect Kengo Kuma, in the form of bamboo walkways, glass walls and a beautiful Japanese garden.

Nearby is the Tokyo flagship store for Sou Sou, a Kyoto-based textile company that produces high-quality artisan fabrics with bold, Marimekko-esque prints. The store is filled with bags, dresses and modern-cut kimono jackets as well as a popular baby and children's range and the brand's signature, handmade, Ninja-style split-toe tabi shoes.

Less swish but no less fashionable, the Nakameguro district, south of the neon blare of Shibuya, appears to inhabit another world entirely despite its location, a quick taxi hop away. Here, quiet low-rise lanes run alongside a river lined with cherry trees, joined by edgy independent fashion boutiques, vintage shops and cafés. A magnet for Tokyo's design community, the neighbourhood bursts into life when the cherry blossom is in bloom and locals set up lanterns and food stalls.

The Harmony Suite at The Spa at Mandarin Oriental, Tokyo

The Harmony Suite at The Spa at Mandarin Oriental, Tokyo

One long-standing resident is Kei Saito, sales director at The Army Gym by Nigel Cabourn, a British label that fits into the area perfectly with its vintage-inspired, military-style clothing and focus on craftsmanship. 'Nakameguro is a secret gem, the best, the friendliest and the most chilled-out destination in Tokyo,' Saito says. 'There's a great mix of people living here, from celebrities to students. Many independent fashion and creative companies are based here, too, as well as vintage stores and hidden bars. Nakameguro is a favourite area of the city among our team.'

Close by, Cow Books is a tiny riverside boutique specialising in out-of-print art and design books, with reading seats and fresh coffee on tap. Other places to visit include concept store 1LDK (named after the term used by Japanese estate agents to describe a one-bedroom apartment), whose layout is like stepping inside someone's home. Here, a carefully-curated selection of Japanese fashion and lifestyle products are on display, including butter-soft leather shoes by Hender Scheme, avant-garde fashion by Cosmic Wonder and minimalist white enamel tableware by Noda Horo.

The Nezu Jinja shrine in Yanaka

The Nezu Jinja shrine in Yanaka

A short stroll away is the perfect spot for a refreshing Japanese tea: Aoya, a small restaurant hidden in an old wooden house at the end of a narrow stone pathway. Try its delicious sweets, including the traditional jelly-like confection warabi mochi and green-tea parfaits.

But as the sun starts to set following a long day of exploring, it's time to head back to Mandarin Oriental, Tokyo – more precisely, to its award-winning Spa, located on the 37th floor with walls of glass. First, soak up the heat in the Japanese communal baths, and then indulge in a signature Oriental Harmony massage. Then, as one skyscraper after another starts to twinkle with light, be sure to lift your head from the massage bed and gaze upon the mesmerising view before you finally drift off to sleep.

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