Originally Setalcott or Setauket, the Town of Brookhaven was already established (beginning about 1655 settlers began purchasing land from the Setauket and Unkechaug Indian tribes) when Suffolk County was officially organized on November 1, 1683. The town was officially incorporated in 1686.
The first settlement in the area was named Setauket. The town boundaries include notable hamlets such as Fire Island Pines and Cherry Grove, Farmingville, Holbrook, Ronkonkama, Setauket, Shirley, Stony Brook, and Yaphank.