John Atherton (1598 - 1640) was born in Somerset, England. He studied at Oxford University and joined the ranks of the Anglican clergy. In 1634 he became Bishop of Lismore and Waterford in Ireland. In 1640 Atherton was accused of buggery, tried, and condemned to death. Reportedly, he confessed to the transgression immediately before his execution, although he had proclaimed his innocence before that.

More recently, some historical evidence has been developed that shows Atherton might have been a victim of a conspiracy to discredit him and his patrons.