Jonathan Oakes was born in Malden, Massachusetts, on October 4, 1751, to Jonathan and Esther (Buckman) Oakes. Before he was 20 years old, Oakes was master of a vessel in the merchant service and later became a naval officer during the American Revolution. In 1776 he was captain of the private armed brigantine Hawke. During the war, he captured several ships.

After the close of the war, he continued in the merchant marine service and in 1796 was the Paris agent for the house of John and Richard Codman of Boston. When he returned home, he retired from seafaring life and became interested in politics. He was elected representative from Malden in the general court of Massachusetts twelve times.

In 1774 Captain Oakes married Sarah Nichols (b. 1754) and they had eight children. Oakes died on August 6, 1818.