It came from the swamp!
The monstrous metropolis that is Tokyo, population 12 million, has come a long way from its origins as a collection of shallows and tidal pools at the mouth of the Sumida-gawa (Sumida River). Fertility was the focus of its first permanent inhabitants and this fecund swampland edging the Kantō plain was perfect for incubating new life. They were a pottery-producing culture who settled here during the late Neolithic Jōmon period (Jōmon means ‘rope marks’ for the design on pottery fragments discovered from this time) around 10, 000 BC. These early Tokyoites lived as fishers, hunters and food-gatherers, and likely benefited from the fauna-rich marshland that was left behind after what is now Tokyo Bay rose to cover most of the valley where Tokyo now sits.
Read more: http://www.lonelyplanet.com/japan/tokyo/history#ixzz3ZRQylpGL