[4] The township is home to two renowned research centers, Stony Brook University and Brookhaven National Laboratory.

Considering this founding year of 1655, Brookhaven is the fifth English township on Long Island following Southampton, Southold, Huntington, and East Hampton.

The original purchase from the native Setalcott tribe that took place in 1655 encompassed the land making up present-day Setauket, Stony Brook, and Port Jefferson.

A second purchase was made by Richard Woodhull in 1664 expanded this tract eastward along the North Shore to additionally include all lands from the Old Mans area (Mount Sinai and Miller Place) to Wading River.

Richard Woodhull was the direct heir of Eustace de Vesci, a British noble who was a signator of the Magna Charta.

Brookhaven was integrated into the Province of New York following that colony's establishment in 1664, and in 1666 Governor Richard Nicolls granted a patent for the town which confirmed title to the lands purchased.

Governor Thomas Dongan issued a patent in 1686 which granted powers to the town and established a representative form of government.

The current seal is a redesign, retaining the original elements, but adding the Town of Brookhaven and its 1655 date of settlement.

Brookhaven was founded primarily by English colonists that partook in the settlement of Southold, and was likewise under the jurisdiction of the theocratic New Haven Colony in the modern state of Connecticut.

Another episode was Benjamin Tallmadge's successful raid from across Long Island to the British stronghold at the Manor St. George, wherein his raiding party rowed from Connecticut to Cedar Beach and marched across Long Island, culminating in the Battle of Fort St. George and burning of the defensive structure.

A more minor skirmish occurred within the settlement of Setauket, where the British had repurposed the local Protestant church as a fortress.

These hosted many urban residents from nearby New York City, including numerous celebrities of the era, during the summer months.

Waterfront areas along the North Shore, including Belle Terre and Old Field, transformed from small fishing communities into fashionable and exclusive enclaves of the moneyed elite.

This was partly due to its proximity to New York City along the Long Island Rail Road and the highway system of Robert Moses.

The township's most internationally renowned institutions, Stony Brook University and Brookhaven National Lab, both date to the years following World War II.

During the mid-century, a number of major transformations were conducted by philanthropist Ward Melville in the "Three Village" area (The Setaukets, Stony Brook, and Old Field).

Melville, an Old Field resident and owner of what later became CVS Corporation, used his fortune to transform Northwestern Brookhaven to his vision of an idealized New England–style region.

In 1962, Ward Melville donated 400 acres of land for the relocation of now-named Stony Brook University from Oyster Bay.

The laboratory contains the Relativistic Heavy Ion Collider (RHIC) and the National Synchrotron Light Source.

Brookhaven is bounded by Long Island Sound to the north, the Atlantic Ocean to the south, Riverhead to the northeast, Southampton to the southeast, Smithtown to the northwest, and Islip to the southwest.

A large part of Fire Island (accessible by a bridge at Smith Point) and the Great South Bay are in the town.

[12] This one-party domination, and a series of scandals, led to a tarnished reputation of local politics and accorded the nickname "Crookhaven".

[18] In 2007, councilwoman Carol Bissonette chose not to pursue re-election, but to instead run for the open receiver of taxes seat.

As per New York state law his seat was declared vacant, a special election was held on March 31, 2009, to replace him.

With Romaine's victory and the subsequent victories of Daniel Losquadro in 2013 for the special election of highway superintendent, and Independence party member Donna Lent to town clerk, the Republican party and its endorsed allies won all townwide seats for the first time since former supervisor John Jay LaValle.

The ferry terminals in Patchogue lead to the communities of Davis Park, and Watch Hill Visitor Center, on the western edge of the Otis Pike Fire Island High Dune Wilderness Area.