The very first known inhabitants of what would later be known as Brookhaven, an area in central Long Island, New York, were Native Americans from the Setauket and Unkechaug tribes. Later, the first English settlers arrived around the year 1640. Brookhaven's geography on the water made it a great place for a settlement. This first English settlement was named Setauket, after the Native American tribe. The names Setauket and Brookhaven were used interchangeably to describe the area during the early years. The official founding year of Brookhaven is considered to be 1655, as that was the year of the first deed of settlement in the town. This made Brookhaven the fifth English town on Long Island, after the towns of Southampton, Southold, Huntington, and East Hampton.

In 1664, a second purchase of land was made by Richard Woodhull, expanding the town. During the same year, Brookhaven was integrated into the Province of New York. This led to Governor Thomas Dongan issuing a patent to establish a representative form of government for the town in 1686, giving the town more power and abilities. Still, the area remained largely agricultural based for many years following. Families lived far apart, and mostly relied on fishing and farming.


The area started seeing more growth in the mid 19th century, when some areas in Brookhaven started functioning as shipbuilding ports. Two of the most successful ports, Port Jefferson and Patchogue, are still two of the towns more popular areas. Around the time the ports were established, railroads also came to the town for the first time, giving more opportunities for growth. Ferries also came, giving another means of transportation.

Later, in the late 19th century, many urban communities on the shores of Brookhaven became the sites of successful resort destinations. The more rural communities also became popular vacation destinations, in the form of campgrounds. Around this time, the area started seeing a lot of economic growth. Many of what used to be small fishing communities started getting turned into exclusive areas for the wealthy.


Following World War II, the town saw a major population boom. This population growth was mostly due to how accessible to New York became to Brookhaven due to new railroads and highways. Two notable institutions were also built around this time, Stony Brook University, and Brookhaven National Lab. Stony Brook Villege Center, a large commercial center, was also built around this time. Brookhaven National Laboratory started operating in 1947. The laboratory has had many notable inventions since it was first established, including the first PET scan, one of the first video games, and a few contributions to particle physics.

As of 2016, the population of Brookhaven is around 486,000 people, making it the most populous town in Suffolk county. Tourism remains a large part of the local economy, and it is the only town that stretches' from the north shore to the south shore of Long Island. Stony Brook University and Brookhaven National Lab remain of large importance in the community, and they are two of the largest employers in Brookhaven.

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