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In the early days of Japan’s railway era, when the history of Tokyo train stations was just beginning, Edward S. Morse boarded a train at Sakuragicho Station in Yokohama, his mind far from archaeology. He had arrived in the port city less than 24 hours earlier, following nearly three weeks aboard a steamship on the Pacific.

It was June, the height of Japan’s rainy season, and he found himself sweating in the humid air while a light drizzle pattered against the hard-packed dirt streets. His journey to the station had been via a curious contraption resembling a horse-drawn carriage—but instead of a horse, a man pulled it along. His minder, an energetic young Japanese man in a three-piece suit holding a bright red paper umbrella, had called the vehicle a jinrikisha.

With a steamy hiss and a bright whistle, the small train clattered away from Sakuragicho. Morse learned that the railway had been completed just five years earlier, in 1872, and that their destination was a place in Tokyo called Shimbashi—a journey that would take precisely 53 minutes. Settling into his seat, he observed his fellow passengers. Some were already asleep, others spoke in hushed tones, and a few gazed at him with open curiosity. Outside the train window, the broad streets and brick buildings of Yokohama soon gave way to wooden huts and rice fields. In the distance, the shimmering waters of Tokyo Bay glowed as sunlight broke through the clouds.

The Omori Shell Mound: Birthplace of Japanese Archaeology

Then, without warning, the train ground to a halt in the middle of nowhere. Facing Morse through the window was a bare rock wall, cut deep into the hillside to make way for the new railway line. He sighed—his first meeting with his new colleagues at the University of Tokyo would now be significantly delayed. With nothing else to do, he stared absently at the rocks before him.

And then he saw them.

Large clumps of broken seashells, embedded in the rock.

A renowned zoologist, Morse instantly recognized them as ancient middens—garbage dumps left behind by prehistoric people. He had stumbled upon one of the most significant archaeological finds in Japanese history.

Morse would go on to lead extensive excavations of the site, later known as the Omori Shell Mound. His discovery sparked the beginning of modern Japanese archaeology, shedding new light on the hunter-gatherer Jomon cultures of prehistoric Japan. Even today, nearly every Japanese schoolchild learns about Omori Kaizuka, as the shell mound is prominently featured in history textbooks.

A Forgotten Station with a Storied Past

JR Omori is my local station in Tokyo, two stops south of Shinagawa and two stops north of Kawasaki on the Keihin-Tohoku Line. It is one of those hundreds of nondescript train stations in the city that people pass through daily without much thought—even those who live nearby. I first learned about Morse’s discovery a few years ago while walking through the pedestrian tunnel beneath the train tracks at Omori. The concrete underpass is adorned with murals depicting Jomon life, complete with images of shell middens and the distinctive rope-patterned (Jomon) pottery that gave the culture its name.

Are you interested in how the Jomon period still influences Japanese culture today? Read our article about the revival of the traditional “tribal” tattoos.

That day, something strange happened.

For a fleeting moment, the city around me—its buildings, overhead wires and reclaimed land—seemed to disappear. In their place, I imagined a different Tokyo, one from thousands of years ago, where distant figures boiled shellfish in clay pots along the shores of a prehistoric bay. A time before rice fields, temples or written language.

How Train Stations Shaped the History of Tokyo

Omori Station first opened in 1876, just a year before Morse’s fateful journey. It was a stop on Japan’s first railway, running from Sakuragicho in Yokohama to Shimbashi in central Tokyo. Without delays like the one Morse encountered, the trip took 53 minutes—only slightly longer than it does today. True to its name (大森 or “big forest”), Omori was sparsely populated at the time. It lay just beyond the roadside inns of Shinagawa that marked the outer limits of Edo, the shogun’s capital. The only notable landmark on contemporary maps was Honmonji Temple. Perched on a wooded hill, the temple overlooked the Tokaido Road as it wound toward Kyoto.

In their book Japan’s Castles: Citadels of Modernity in War and Peace, historians Oleg Benesch and Ran Zwigenberg describe how the advent of railways in Japan reshaped the country’s urban centers. Traditionally, Japanese cities were built around castles, but the railway revolution shifted their focal points outward—to train stations. Omori, once covered in forests, grew into a residential neighborhood. Yokohama, once a tiny fishing village, transformed into Japan’s second-largest city. Across Tokyo, train stations became the seeds from which neighborhoods sprouted—some evolving into neon-lit hubs like Shibuya, Ikebukuro, and Shinjuku, while others remained quiet commuter towns.

Today, nothing defines Tokyo more than its trains and their stations.

Morse’s discovery at Omori reminded me that every station has a story. His lucky train delay unearthed a prehistoric past hidden beneath the modern city. And it made me wonder—how many more untold stories lie buried in the stations of Tokyo, just waiting to be rediscovered?

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Unsure how to navigate Tokyo’s train culture? Read our article about mastering Japanese train etiquette.