The written history of Boston begins with a letter drafted by the first European inhabitant of the Shawmut Peninsula, William Blaxton. This letter is dated September 7, 1630, and was addressed to the leader of the Puritan settlement of Charlestown, Isaac Johnson. The letter acknowledged the difficulty in finding potable water on that side of Back Bay. As a remedy, Blaxton advertised an excellent spring at the foot of what is now Beacon Hill and invited the Puritans to settle with him on Shawmut.

Boston was named and officially incorporated on September 30, 1630 (Old Style). The city quickly became the political, commercial, financial, religious and educational center of Puritan New England and grew to play a central role in the history of the United States.

When harsh British retaliation for the Boston Tea Party resulted in further violence by the colonists, the American Revolution erupted in Boston. Colonists besieged the British in the city, fighting a famous battle at Breed's Hill in Charlestown on June 17, 1775—a battle lost by the colonists but one that inflicted great damage on British forces. The colonists later won the Siege of Boston, forcing the British to evacuate the city on March 17, 1776. However, the combination of American and British blockades of the town and its port during the conflict seriously damaged the economy, leading to the exodus of two-thirds of its population in the 1770s.

The city recovered after 1800 and re-established its role as the transportation hub for New England with a network of railroads. Beyond a renewed economic success the re-invigorated Boston became the intellectual, educational and medical center of the nation. Along with New York, Boston became the financial center of the United States in the 19th century, and the large amount of capital available there for investment was crucial in funding the expansion of a nationwide railroad.

During and before the Civil War Boston was the launching pad and funding base for many of the country's anti-slavery activities. In the 19th century city politics and society became dominated by a financial elite known as the Boston Brahmins. This entrenched power base squared off against the political challenge of more recent Catholic immigrants for the rest of the 19th century. Wealthy Irish Catholic political dynasties, typified by the Kennedy Family, assumed political control of the city by 1900. This control has been substantially maintained for more than a century, however this power has swayed as Boston continues to become more diverse.

The industrial base of the region, financed by Boston capital, reached its zenith around 1950. The city went into decline after the middle of the 20th century when thousands of textile mills and other factories were closed down as the United States began a long deindustrialization. By the early 21st century the city's economy recovered, moving from an industrial base to one centered on financial services, education, medicine, and high technology, especially biotechnology startups. The many towns surrounding Boston became residential suburbs that now house the city's large population of white collar workers.

Indigenous era Prior to European colonization the region around modern-day Boston was inhabited by the Indigenous Massachusett people. Their habitation consisted of small, seasonal communities along what is now the Charles River. The river was accurately named Quinobequin in the Algonquin language of the Massachusett, and they knew it as "the meandering one". The people who lived in the area most likely moved between inland winter homes along the meanders of the Charles and summer communities on the coast. Game was most easily hunted inland during bare-tree seasons while the fishing shoals and shellfish beds on the tidal flats of Boston harbor were more comfortably exploited during the summer months.

Being surrounded by mudflats and salt marshes, the Shawmut Peninsula itself was more sparsely occupied than its surroundings before the arrival of Europeans. Nevertheless, archeological excavations have revealed one of the oldest fish weirs in New England on Boylston Street. Native people constructed this weir to trap fish as early as 7,000 years before European arrival in the Western Hemisphere.

The Shawmut Peninsula was originally connected with the mainland to its south by a narrow isthmus, Boston Neck, and was surrounded by Boston Harbor and Back Bay, an estuary of the Charles River. This neck of land was surrounded by infill beginning in 1803 and expanded to dozens of times its original width by the turn of the 20th century.

Foundation by Europeans

Blaxton Era (1624–1630) The first European to live in what would become Boston was William Blaxton. He was directly responsible for the foundation of Boston by Puritan colonizers in 1630. Blaxton had joined the failed Ferdinando Gorges expedition to America in 1623, which never landed. He eventually arrived later in 1623, as a chaplain to the subsequent expedition of Ferdinando's son, Robert Gorges, aboard the ship Katherine. This expedition landed in Weymouth, Massachusetts, five miles south of what is now Boston.

By 1625 the colony at Weymouth had failed and all of his fellow travelers returned to England. Blaxton remained, moving five miles north to a 1 mi2 rocky bulge at the end of a swampy isthmus surrounded on all sides by mudflats. Blaxton thus became the first colonist to settle in what would become Boston. He lived at the Western end of the Shawmut Peninsula at the foot of what is now Beacon Hill and was entirely alone for more than five years.

Puritan Era (1630–1750)

Invitation from Blaxton In 1629 Isaac Johnson landed with the Puritans in nearby Charlestown, having left Salem for want of food. Blaxton and Johnson had been university contemporaries at Emmanuel College, Cambridge. The rockier highlands of Charlestown lacked easily tappable wells. Knowing of this difficulty, Blaxton wrote a historic letter in September 1630 to Johnson and his group of Puritans that advertised the peninsula's excellent natural spring, and invited them to settle on his land. This they did over the course of September 1630.

Renamed "Boston" One of Johnson's last official acts as the leader of the Charlestown community before dying on September 30, 1630, was to name the new settlement across the river "Boston." He named the settlement after his hometown in Lincolnshire, from which he, his wife (namesake of the Arbella) and John Cotton (grandfather of Cotton Mather) had emigrated to New England. The name of the English city ultimately derives from that town's patron saint, St. Botolph, in whose church John Cotton served as the rector until his emigration with Johnson. In early sources the Lincolnshire Boston was known as "St. Botolph's town", later contracted to "Boston". Prior to this renaming the settlement on the peninsula had been known as "Shawmut" by Blaxton and "Trimountaine" by the Puritan settlers he had invited.

Settlement on Shawmut Peninsula The Puritans settled around the advertised springs on the north side of what is now Beacon Hill (at the time called "Trimountaine" from its three peaks). Blaxton negotiated a grant of for himself in the final paperwork with Johnson, amounting to around 10% of the peninsula's total area. However, by 1633 the new town's 4,000 citizens made retention of such a large parcel untenable and Blaxton sold all but six acres back to the Puritans in 1634 for £30 ($5,455 in adjusted USD). Governor Winthrop, Johnson's successor as leader of the settlement, purchased the land through a one-time tax on Boston residents of 6 shillings (around $50 adjusted) per head. This land became a town commons open to public grazing. It now forms the bulk of Boston Common, the largest public park in present-day downtown Boston.

After Johnson's death the Episcopalian Blaxton did not get along with the Puritan leaders of the Boston church, which rapidly became radically fundamentalist in its outlook once it began executing religious dissidents such as Quakers. In 1635 Blaxton moved about south of Boston to what the Indians then called the Pawtucket River and is today known as the Blackstone River in Cumberland, Rhode Island. He was that region's first European settler, arriving one year before Roger Williams established Providence Plantations.

Original topography of the peninsula The peninsula on which the Puritans settled was rocky scrubland with few trees. It held three major hills: Copps Hill (now the North End), Fort Hill (later the Financial District), and Trimountaine (Beacon Hill). Trimountaine was the tallest of the three, with its name coming from its three separate peaks. The name was retained for the hill and in later years Trimountaine would be shortened to Tremont, for which Tremont Street was named.

The three peaks of Trimountaine were,

Cotton Hill—named for John Cotton, and later renamed Pemberton Hill (now Pemberton Square), Centry or Sentry Hill—the present location of the Massachusetts State House, and Mount Whoredom—also known as Mount Vernon, now the location of Louisburg Square, home to some of the most expensive real estate in the nation.

Over the next two centuries the three hills would be regraded and the geography of the area transformed through landfill and annexation. Beacon Hill or Trimountaine, though shortened between 1807 and 1824, remains a prominent feature of the Boston cityscape. It received its current name from the signal beacon erected on its highest peak to warn outlying towns of danger.

Response to 1684 charter revocation

In 1684, fearing that the rumored revocation of the Massachusetts Bay Colony's Charter by King Charles II would come to pass, Boston city fathers sought to buttress their fifty year old claim to the land of the Shawmut Peninsula. To this end in early 1684 they attempted to secure legal ownership of the Shawmut Peninsula from the descendents of Chickatawbut (d. 1633), the Massachusett sachem at the time Blaxton first settled on the peninsula, fifty years prior. Such a descendent was located, a sachem named Josias Wampatuck. There is little evidence that this sachem, his grandfather Chickatawbut or any of their people ever inhabited the peninsula, however the lack of formal legal documents involving Indians during the Blaxton transactions encouraged the creation of a backdated deed (known in English common law as a "quitclaim") which Josias duly signed on March 19, 1684 (see document at right, and its transcription). The charter was revoked as promised later that year on the advice of colonial administrator Edward Randolph.

Colonial era

Early colonists believed that Boston was a community with a special covenant with God, as captured in Winthrop's "City upon a Hill" metaphor. This influenced every facet of Boston life, and made it imperative that colonists legislate morality as well as enforce marriage, church attendance, education in the Word of God, and the persecution of sinners. One of the first schools in America, Boston Latin School (1635), and the first college in America, Harvard College (1636), were founded shortly after Boston's European settlement.

Town officials in colonial Boston were chosen annually; positions included selectman, assay master, culler of staves, Fence Viewer, hayward, hogreeve, measurer of boards, pounder, sealer of leather, tithingman, viewer of bricks, water bailiff, and woodcorder.