Samuel Pepper was born in Woodford County, Kentucky, on 10 October 1802, the son of Elijah Pepper (1769-1831) and Sarah Neville O’Bannon (1770-1848). On 5 February 1824, Samuel married Mahala E. Perry (1804-1865), the daughter of Roderick Perry (1776-1821) and Susanna Brown Perry (1776-1853). Mahala and Samuel had grown up on adjoining farms and knew each other all their lives. In 1831, Samuel and Mahala moved into a newly built home later dubbed Sweet Lawn. On their farm they raised corn and other grains used in the bourbon whiskey produced at a nearby distillery that was the Pepper family business.
Samuel and Mahala had four children who reached adulthood. In 1864, the couple decided to move to nearby Frankfort, Kentucky’s capital. In March 1865, Mahala, at age 61, died in Frankfort, and two weeks later Samuel sold Sweet Lawn to his daughter, Mary Louise Pepper and son-in-law Joseph Eccles McCoun. Samuel lived nine more years then on 16 October 1874 died at the home of their son, Robert Perry Pepper.

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