The New England colonists of the 17th and 18th centuries were English people, in English colonies, so their colonial flags were based on English flags.

The English Flag.

When the New England colonies were started, England was a kingdom, ruled by a king.  Before the English Civil War (1649-1660) the King effectively "owned" the country. His flag, the flag of flag of England, was a white field with the red cross of St. George.

In contrast to England, the flag used by the King of Scotland was the cross of St. Andrew.  The Scottish flag is shown on the right.

The English Naval Ensign before 1707.

Often the flags flown by ships, known as "ensigns," or "jacks" are variations of the country's flag. (An ensign is flown on the main mast; a jack is flown on the bow of the ship, but we will skip the niceties of where and how and who can fly a jack. It's not a part of this article.) From about 1600 to 1707 the English Navy ships used a Naval Ensign which was a highly visible red flag with a canton in the upper left containing the King's Colors, to wit: the red cross of St. George. 

The Massachusetts Bay Colony was formed when this English Naval Ensign was the common flag available on both English Navy and merchants ships and also in overseas colonies. Thus, when the Massachusetts Bay Colony was started in New England in 1630, this English Navel Ensign became the first flag flown on official occasions by the Colony.

Virginia, and the other English colonies, as they were formed,  generally used  the English Naval Ensign with  --- the  cross of St. George --- as  their flag.

The Massachusetts Bay Colony Flag (Used1636 to about 1686).

Started in 1630, the Massachusetts Bay Colony originally used the 1630  English Naval Ensign.  However, a religious problem arose. The  Massachusetts Bay Colony was the home of thousands of religious dissenters who came over to the New World to make get away from the Catholic Church and the Church of England. The ministers condemned the traditional "idols" of the the Catholic Church and the Church of England.  In 1636, in a sermon in the Massachusetts Bay Colony, Roger Williams (before he was banished and fled to Rhode Island) fastened on the cross of St. George as an "idol" and condemned the use of the St. George's cross in the colony's flag. The Governor of the Colony, John Endicott, ordered the Standard Bearers of the Colony (many towns in the Colony had an official named the Standard Bearer)  to remove the St. George's Cross from their flags. Before this was done, however, the Great and General Court of the Colony decreed that  Endicott's order changing the flag "exceeded the lymits of his calling", removed him from office, and forbid him holding any public office for one year. However, being composed of practical politicians, The Great and General Court of the Colony gave the Standard Bearers permission to devise any kind of flag they wanted. Without exception, the Standard Bearers removed the crosses from their flags.

From Endicott's of 1636 order until about 50 years later, the unofficial flag of Massachusetts Bay was red with an blank white canton. By the late 1600's, in New England they weren't quite so sure that the King's personal official flag of St. George was un-Christian, and the St. George's cross again began to appear on  flags. This solved the bland style of a barren white canton, and showed loyalty to the person of the King of England.

The (English) Union Flag.

In 1707, England and Scotland were reunited under one king. Thus, to the flag of the King of England was added the flag of the King of Scotland.  (See illustration on the right of the result. Notice that the resulting flag was not the present flag used by the United Kingdom of England, Scotland, and Ireland, which "UK" never existed before the United States was formed.)  The Union Flag and the Union Jack (see below) generally were not used in the colonies, which by that time wanted to have a separate identity from the island of England.

The Union Jack (The English Naval Ensign after 1707).

After the 1707 reunion of England and Scotland, and the subsequent change in the "King's Colors", the English Royal Navy used a Union Jack which was a red flag with a canton in the upper left with the King's "unified" flag.

The Union Jack was associated with English Navy ships. As to English-owed merchant ships, in 1674 a royal proclamation had ordered English merchant ships to use the English flag of the day, the plain white flag with the red cross of St. George.  Although presently much ignored the 1674 regulation never has been cancelled, so some English ships still occasionally fly the plain white flag with the cross of St. George

New England Ships' Ensigns.

By the time the Union Jack was used by English Navy ships, the pine tree had become a core symbol of New England. The pine tree indicated not only a prime export (lumber) but also the nature of the New World.  The tree started appearing on local coinage, and eventually on the flags used on merchant ships the colonists built and sailed on merchant voyages to various places in the New World as well as to Europe.  Sometimes New England ships used a plain white flag with a green tree of some sort shown on it, commonly a pine tree. The New England merchants and ship captains wanted  their ships in port to be clearly understood as ships sailing to/from New England. In a busy port, or in a port looking for New England fish, lumber, or rum, this was an advantage.

Instead of the plain white flag with a green tree, the more substantial ship owners of New England (with their larger ships) tended to use a variation of the Union Jack. The variation substituted a green tree for the Union Flag in the upper left white canton of the flag used by English Navy ships.

At the same time, by the late 1600's-early 1700's, in New England they weren't quite so sure that the King's cross of St. George was un-Christian, and the St. George's cross again began to reappear in the white canton on  flags.

A combination of the "King's" cross of St. George and a pine tree eventually evolved. In a 1686 manuscript, Insignia Navalia by Lt. Gradon, an illustration of the "New England Jack" appears, showing it as a plain white flag with a red St. George's Cross but with an Oak tree in the extreme upper left. Other documents from approximately this time period show the ship's flags of ships of the New England colonies as being a flag with a white canton in which there was both the red St. George's Cross and a green tree (usually pine or oak) in the extreme upper left of the canton.

By the French and Indian War (1756 - 1763) the ensign shown on the left (with the red St. George's Cross and a green tree in the white canton) was the one most frequently flown by the ships of Rhode Island and the Massachusetts Bay Colony. Those two colonies dominated trade to and from the English New England colonies.  Thus, by the time just preceding the American Revolution the flag identified by many with New England as a region was that ship flag.

When the Revolution came, the Massachusetts colony in 1775 declared its official  Massachusetts Navy flag to be this naval ensign (the one first above).  About the same time, George Washington’s military secretary, Colonel Joseph Reed, proposed that all American ships fly a red flag with a plain white canton with only one green pine tree in it (the second one above), so that all American ships could recognize one another. His proposal was not adopted.

Sons of Liberty Flags.

The Sons of Liberty originally used a flag of 9 vertical stripes to represent the unity of the New England colonies that corresponded regularly with each other regarding measures to be taken regarding the English Stamp Act.

The history of a flag identifying the Sons of Liberty flag began in 1765, when protests of the duties and taxes and stamps required by Parliament began in the colonies. The Sons of Liberty took their name from a debate on the Stamp Act in Parliament in 1765. Members of Parliament included several prominent Members supportive of the American view that the tax was improper, William Pitt (the Elder), Charles James Fox, and Edmund Burk. During the debate, Charles Townshend, speaking in support of the Stamp Tax Act, spoke  of the American colonists as being "children planted by our care, nourished up by our indulgence...and protected by our arms." Isaac Barre, member of Parliament and friend of the American colonists, countered with a severe reprimand in which he spoke favorably of the Americans as "these Sons of Liberty."

In Massachusetts, after a particular protest of the Stamp Act was held under a particular Elm tree in Boston, known thereafter as "the Liberty Tree," a group known as the Sons of Liberty was formed. They met regularly under the tree. The English Army cut the tree down. The Boston people erected a pole and flew the nine-striped "Sons of Liberty" flag from it.

Among other things to protest the Stamp Act, nine colonies sent delegates to their "Stamp Act Congress"  They petitioned the King and Parliament; the Act was repealed in 1766. The flag of nine red and white stripes that represented these "Sons of Liberty" became known in England as the "Rebellious Stripes."

After the Stamp Act was repealed by the English Parliament, the Sons of Liberty erected a Liberty Pole in New York City to celebrate the repeal of the Stamp Act. There was a long-running skirmish over these Liberty Poles with the British troops stationed there (the most notable engagement being the Battle of Golden Hill on January 19, 1770). As poles were alternately erected by Patriots and cut down by troops, violent outbreaks over it raged intermittently from 1766 until the Patriots gained control of New York City government in April 1775. The last liberty pole was cut down by occupying British troops on October 28, 1776.

After the successful effort to repeal the Stamp Act, the nine- striped flag was modified to 13 horizontal stripes to represent the unity of all the colonies.  That 13-striped flag  became the one enshrined in our popular culture.  Among other things, it was used as a United States merchant ship ensign during the American Revolution.

to read about more American colonial flags, the first flags of the combined Colonial Army, Navy, and Marines, plus the first official Stars and Stripes