Plymouth Colony and the Massachusetts Bay Colony were two distinct Puritan commonwealths. Because this fact is not widely known, it is useful to understand some of the distinctions.
The Plymouth Colony was founded by the Pilgrims, who arrived in Massachusetts on the Mayflower in 1620 and celebrated the first Thanksgiving, which was a harvest festival , the following year. The colony lasted from 1620 to 1691.
Like all Puritans, the Plymouth settlers were Calvinists desiring a single, purified, reformed faith reflective of the early Christian church, as well as the elimination of residual traces of Roman Catholicism from the Church of England (i.e., Anglicanism, which in the United States became Episcopalianism).
The Pilgrims were a subset of Puritans known as Separatists. Convinced that the Church of England could not be reformed from within, they seceded from the Anglican Communion to found their own churches. Many moved to Holland.
Because the Church of England was the official and only church in England—indeed, an extension of the government—everybody belonged to it. Every resident of a community was automatically a member of the parish in his community.
The English parish system thus encompassed all citizens indiscriminately, without regard to character, beliefs, or true degree of Christian commitment. Of course, the same was true in other regions with state churches, such as Lutheran Scandinavia.
According to Separatist convictions, this was contrary to a “communion of saints.” The church should be composed only of religiously dedicated Christians.
Two Puritan Colonies
Plymouth ultimately proved less successful than its neighbor to the north, the Massachusetts Bay Colony, which was founded 10 years later in 1630 and also ceased to exist in 1691. When people talk about Puritan influence in America, they are referring, albeit usually unwittingly, to the Puritanism of the Massachusetts Bay Colony, not Plymouth or the Pilgrims.
Boston was the chief center of the Bay Colony. Colonial jurisdiction eventually extended to much of present-day New England, including portions of Massachusetts, Maine, New Hampshire, Rhode Island, and Connecticut. The Colony’s leading figure was John Winthrop.
William Bradford’s Plymouth Colony was from the start more tolerant than its neighbor. Although witchcraft, for example, was a capital offense in Plymouth, only two charges for the crime were ever brought. The first was dismissed before trial; the second resulted in the acquittal of the defendant and punishment of the accuser for making false allegations.
But even Massachusetts Bay itself was a remarkably argumentative and politically contentious society, where authority was frequently and vigorously contested. Despite his great natural leadership gifts and authoritarian style, for example, John Winthrop was deposed more than once.
The two colonies differed in other important ways.
The Massachusetts Bay colonists were committed to reforming the Church of England from within rather than separating from it. The Church of England remained the official church.
However, as a practical matter, there was no ecclesiastical hierarchy to sustain a state church bureaucracy. During the entire colonial period, for example, not a single Anglican bishop was appointed to rule the American flock.
Thus, over time, migration from England brought about de facto separatism in Massachusetts Bay, and the adoption of Plymouth Colony’s Congregational form of church polity, wherein each local congregation controlled its own affairs.
There were also significant wealth and status differences between the two populations.
The Pilgrims at Plymouth were mostly farmers and artisans. The colonists of Massachusetts Bay, in contrast, were better educated, more economically and socially successful, and brought with them educated clergy to provide leadership for both church and community.
Massachusetts Bay’s governor, John Winthrop, was the son of a Suffolk squire, a neighbor and friend of the Earl of Warwick, a Cambridge graduate, and a trained attorney. English historian Paul Johnson called him “the outstanding figure of the Puritan voyages, the first great American.”
Effects of the Great Migration
Demographically, Massachusetts Bay, though founded a decade after Plymouth, quickly grew much larger. Migration to the Bay Colony far exceeded that to Plymouth.
The Mayflower arrived at Plymouth in November 1620, at the very onset of winter, carrying 102 passengers, 45 of whom (44%) died during the first few months.
Indeed, by November 1621, one year later, only 53 pilgrims remained alive to celebrate the First Thanksgiving. Of the original 18 adult women, 13 died within a few months of arrival, while another died in the spring of 1621. Thus, only four adult women were alive to attend the Thanksgiving festival.
Though somewhat obscured by the effects of subsequent immigration and inter-colonial population movement, the comparatively small size of Plymouth Colony throughout its history suggests that it experienced both founder effects and a severe population bottleneck  at the outset of its existence. Subsequently, survivors exhibited high fertility.
In contrast, no fewer than 11 ships headed by the Arbella and known as the Winthrop Fleet , the first in a great series of convoys, made port in Massachusetts Bay in 1630, carrying 700 Puritans. In the summer of 1634, 20 ships with 2,000 settlers arrived.
The Puritan Great Migration of 1620–1640 refers to the large out-migration of Englishmen, primarily Puritan families, to Massachusetts, the islands of the West Indies, and elsewhere.
Roughly 80,000 people left England during those two decades—the greatest emigration from the country to that time. Twenty thousand went to New England, primarily to Massachusetts Bay Colony, 20,000 to the Netherlands, 20,000 to Ireland, and 20,000 to the West Indies, especially sugar-rich Barbados.
After a few decades, the population of Plymouth Colony was 2,500, compared to Massachusetts Bay’s 20,000. Following the revocation of the Edict of Nantes in 1685, Massachusetts Bay also experienced an influx of French Protestant Huguenots.
The population of Plymouth at the time of both colonies’ dissolution by royal edict in 1691 is estimated to have been only 7,000.
The advent of the English Civil War in the early 1640s brought the Great Migration to an end. An estimated 7 to 11 percent of the population returned to England, some to fight in the Civil War.
Puritan authorities in Massachusetts were sympathetic to the Parliamentary cause, and had generally positive relationships with the governments of the English Commonwealth and the Protectorate of Oliver Cromwell.
The End of the Puritan Experiment
Following the English Restoration in 1660, the royal administration took steps to supersede Puritan rule. Massachusetts Bay in particular was reluctant to admit that the king had the authority to control its governance. This led to crises in the 1660s and late 1670s.
The old New England colonies were finally dissolved, and in 1691 a royal charter issued establishing the new “Province of Massachusetts Bay.” The Massachusetts Bay Colony, Plymouth Colony, Martha’s Vineyard, Nantucket, present-day Maine, New Brunswick, and Nova Scotia were by this act merged into a single political entity.
The new charter, which formally extended voting rights beyond the Puritan sect, brought the commonwealths of Plymouth and Massachusetts Bay Colony to an end less than a century after their beginning.
As psychologist Kevin MacDonald has summarized:
The main source of Puritan decline was that the British government denied them the right to police their borders and expel heretics. In 1664 the British government ruled that an Englishman need not be a member of the Congregationalist Church to qualify as a freeman in Massachusetts. The Charter of 1691 prescribed freedom of Christian religious conscience (except to Papists!); it also ended the colony’s right to select its own governor, limit voting to church members, and expel heretics. And as political control waned, it became increasingly difficult to impose Puritan religious and moral orthodoxy on the inhabitants of New England. After 1650, the [Massachusetts Bay] colony was inundated by waves of immigration by people who were not committed to the Puritan way of life—more inclined to commercialism and materialism. There was also a diminution of Puritan militancy, perhaps because of its extraordinary demands for conformity, emotional intensity, and self-denial. For all practical purposes, the dream (i.e., the group evolutionary strategy) had ended within 70 years after its beginning. (“Diaspora Peoples,” preface to the paperback edition of A People That Shall Dwell Alone, 2002; the Puritans are one of the “diaspora peoples” discussed.)
By the time of the American Revolution, religious tolerance in New England was the norm.
Boston natives John Adams and Benjamin Franklin, both descendants of Massachusetts Bay Puritans, exemplified the process. Adams explicitly and favorably remarked upon the liberalism of religious belief in New England during his time, and his descendants Brooks Adams and Charles Francis Adams criticized John Winthrop and the Massachusetts Bay colonists for their authoritarianism and propensity to persecute religious opponents.
Knowledge of the Puritans
Detailed contemporary records of the Puritan colonies in Massachusetts survive, two well-known examples of which are William Bradford’s Of Plymouth Plantation and John Winthrop’s General Observations for the Plantation of New England.
Paul Johnson states that
These diaries and letters, which are plentiful, and the fact that most important documents about the American colonies have been preserved, mean that the United States is the first nation in human history whose most distant origins are fully recorded. For America, we have no ancient national myth or prescriptive legends but solid facts, set down in the matter-of-fact writings of the time. We know in considerable detail what happened and why it happened. And through letters and diaries we are taken right inside the minds of the men and women who made it happen. (A History of the American People, 1997, p. 32)
With respect to Plymouth Colony, mention should be made of the work of John P. Demos, who first examined in detail physical artifacts, wills, estate inventories, and a variety of legal and official enactments, in the process dispelling several myths about early American Puritans.
His book, A Little Commonwealth: Family Life in Plymouth Colony (New York: Oxford University Press, 1970; thirtieth anniversary edition with a new foreword by the author, 2000) has been described by one academic  as
its own kind of publishing phenomenon. Demos’s work on family life in Plymouth Colony began with a graduate seminar paper, which developed into an article in the William and Mary Quarterly [“Notes on Life in Plymouth Colony,” April 1965] , which led in turn to an invitation to expand the work into a pamphlet for Plimoth Plantation. The proposed pamphlet grew into a book-length manuscript—which was then rejected by the publisher for whom it was intended. (Somewhere out there is one deeply chagrined publishing executive.) But Oxford University Press accepted the manuscript and published it in 1970. It has been in print ever since, and Oxford has just issued a thirtieth-anniversary edition with a new foreword by Demos. In our age of shrinking backlists, small press runs, and short in-print lives, A Little Commonwealth is a rara avis: appealing to general readers, admired by scholars, praised as innovative and provocative when it first appeared, and now well established as a classic in early American history.
Despite the sharp distinctions between the two Puritan colonies, even people as highly placed as Presidents Ronald Reagan, George H. W. Bush—a Mayflower descendant—and their speechwriters often confuse them.
Others, who know better, sometimes denigrate the Plymouth colonists:
To the Pilgrims was due the fact that the congregational way of organization and worship became the accepted form in Massachusetts [Bay] and Connecticut. But in other respects Plymouth was vastly overshadowed by her vigorous neighbors. Her people, humble and simple, were without importance in the world of thought, literature, or education. Their intellectual and material poverty, lack of business enterprise, unfavorable situation, and defenseless position in the eyes of the law rendered them almost a negative factor in the later life of New England. No great movement can be traced to their initiation, no great leader to birth within their borders, and no great work of art, literature, or scholarship to those who belonged to their unpretending company. (Charles M. Andrews, The Fathers of New England: A Chronicle of the Puritan Commonwealths [Yale University Press], 1919, pp. 19–20)
Such a view, whether accurate or not, is ironic in light of the importance attached to genealogical descent from Mayflower Pilgrims.