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Samuel Willoughby (August 20, 1730 – between 1776 and 1790) was a physician and political figure in Nova Scotia. He represented Cornwallis township in the Nova Scotia House of Assembly from 1760 to 1765 and from 1770 to 1776.
He was born in New London, Connecticut, the son of Joseph Willoughby and Thankful Bliss. He received a land grant in Cornwallis, where he is believed to have set up practice. Willoughby is thought to have been the first physician in King's County after the expulsion of the Acadians. Willoughby married Alice English in 1760. In 1768, he was named a justice of the peace for King's County. Willoughby was also a member of the first Masonic lodge in the county. In 1776, his seat in the assembly was declared vacant for non-attendance.