Hanover Township marks the spot of the first settlement in all of northwest New Jersey. New Englanders established a settlement along the Whippany River in 1685 near the current location of the old Whippany Cemetery on Route 10.

Once the Province of West Jersey purchased the land from the local Lenape Native Americans, the original County of Morris was created and comprised all of what is now Morris, Sussex and Warren Counties. It was itself divided into Townships. One of its Townships was 'Whippenny' which itself comprised all of what is now Morris County.

The name Hanover was taken from the House of Hanover in Germany. This namesake was given to the Township of Hanover on December 7, 1720, as a sign of respect to George I of Great Britain who was of the House of Hanover and who ruled over the American colonies in the eighteenth century. Since the creation of Hanover Township in 1720 and its incorporation on March 25, 1740, its size has been considerably decreased as the population of the area has increased. Originally encompassing all of Morris County and parts of Sussex and Warren County, Hanover Township became too unwieldy for a single local government to maintain. The Township was subdivided into smaller municipalities that could provide more responsive local control despite placing greater demands on the local tax base to support new facilities for each.

Portions of the township were taken to form Mendham Township on March 29, 1749. Hanover Township was established by an Act of the New Jersey Legislature on February 21, 1798. Additional portions of the township were taken to form Chatham Township (February 12, 1806), Rockaway Township (April 8, 1844), Boonton Town (March 16, 1866), Mountain Lakes (April 29, 1924), Morris Plains (April 15, 1926), East Hanover Township and Parsippany-Troy Hills Township (both on May 9, 1928).

During the Revolutionary War, George Washington and his troops often camped in, and marched through, Hanover Township.

The name Whippany is a corruption of the Native American word Whippanong which means "where the willow trees grow".

The old villages of Monroe and Malapardis were consumed by development and what remains are two communities - Whippany and Cedar Knolls - which are roughly separated by Interstate 287.

The Malapardis area of Cedar Knolls is primarily located around Malapardis Road. A section of Malapardis, even though it is in Hanover Township's boarders, has a Morris Plains mailing zip code. Another section of Cedar Knolls is called Trailwood which has a section of its land in a Morris Plains ZIP code, the area closest to American Way.

The Monroe area of Whippany is located around Whippany Road and Cedar Knolls Road, marked by a building in the intersection named Monroe Hall.

Until the post-World War II suburbanization of New Jersey, Hanover Township was a sparsely populated industrial town known for its iron works and paper mills. This industry was driven by the ever-present power of the Whippany River. Over the second-half of the twentieth century, the Township became thoroughly suburban.

Lucent Technologies had a large facility in Whippany. The first demonstration of long distance television transmission in the United States took place in 1927, with a transmission that went via wire from Washington, D.C., to New York, and from Whippany to New York using radio.

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