Dressed in a crisp white jacket, white shirt and black tie, bartender Gen Yamamoto looks as though he has just emerged from a casino in a James Bond film. Inside his eponymous bar, which opened in February, the atmosphere is one of cool tranquility. The earth-toned walls complement the heavy, dark-wood bar, fashioned from a 500-year-old Mizunara tree, and the only decoration is a small vase filled with yellow blossoms in a nook near the entrance. There’s no background music, just the tinkle of ice cubes and the sound of Yamamoto’s wooden muddler transforming a tomato into the base of a cocktail.

“This is a Kakegawa tomato from Shizuoka Prefecture,” he says, gently extracting the juice from the fruit before stirring in a dollop of tomato confiture and a shot of Kawabe komejōchū (shōchū made from rice). He points out that tomatoes originally come from Latin America, “so the farmer is trying to create a similar environment to give his tomatoes dense flavor.”

A native of Mie Prefecture, Yamamoto switches effortlessly between Japanese and English, which he mastered during his eight-year stint as a mixologist in New York City. Before returning to Japan last year, he managed the bar at Brushstroke, a high-end Japanese restaurant opened by celebrity chef David Bouley, where he gained a reputation for creating surprising cocktails with fresh produce found at farmers markets.

At times, Yamamoto sounds more like a chef than a bartender. He talks about base notes, texture, pH balance and the effect of soft water on crops. The inspiration for his cocktails comes from the natural ingredients he selects, and the recipes — which he changes to match the seasons — frequently include homemade syrups, compotes or salts he prepares himself. Although he also serves drinks à la carte (from ¥1,500), most of the guests opt for his four- or six-cocktail tasting menus (¥4,200 and ¥5,800).

On my first visit, Yamamoto presented me with a ruby-hued concoction of strawberries from Tochigi Prefecture and Amaneko sake, finished with a sprig of kinome (Japanese pepper leaf) and served in a delicate hand-blown glass. The next “course” was an eye-opening cocktail of ginger and lime from Ehime Prefecture — mixed with London Hill gin and Yamamoto’s spiced ginger syrup, spiked with clove and sanshō (Japanese pepper) — followed by a refreshing cucumber-and-gin cocktail, in a cup rimmed with toasted almond salt.

But the showstopper was the tomato cocktail. It was sweet and intensely perfumed, the platonic ideal of what the Japanese call furūtsu tomato (tomatoes containing high levels of fructose), with layers of umami complexity unfolding across the palate. The sweetness, Yamamoto explains, is completely natural. He concentrates the sugars by slowly simmering the tomatoes until they reach the consistency of jam.

When I returned to the bar a couple of weeks later, Yamamoto served me a different version of the tomato cocktail. In this one, he had used gin and shiso (perilla) buds to give the drink a brighter character. He’d altered the recipe to show me a different side of the fruit. Like all great bartenders, Yamamoto doesn’t simply mix drinks: He tries to tell a story.

For more information, visit www.genyamamoto.jp. Melinda Joe is an American journalist in Tokyo and a certified wine and sake professional. She blogs at tokyodrinkingglass.blogspot.com. Follow her on Twitter @MelindaJoe.

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