Following graduation, Jonathan took a position as clerk in the law office of John Ruggles of Thomaston. While he studied law, he roomed with the family of Hezekiah Prince and soon found himself falling in love with Deborah, one of the Prince daughters. Politics, in which Mr. Ruggles was active, became an ambition of his. After marrying Deborah, Jonathan ran for office on the state level. He was soon chosen to serve in the Maine Legislature and eventually rose to the position of Speaker of the Maine State House. From that position it was a short step to election as Representative from Maine to the United States Congress.

Shortly after his term in Washington began, Jonathan was challenged to a duel by a Representative from Kentucky, William Graves. The basis for the duel was that Jonathan had asked, during a debate in the House, whether or not a certain publisher was the same man who, years earlier, had changed his newspaper's editorial position after receiving an unauthorized loan from the Second Bank of the United States. He commented that such a man could not be trusted to tell the truth. That question and comment led to the challenge after the editor came to Washington to "defend his honor." Cilley refused to accept a note from the editor and refused, as well, to make a public statement saying that the editor was an honest man and a gentleman. He said that he could not vouch for the character of any person he did not know. Eventually, Cilley was forced into accepting the challenge when it was said that he needed to "preserve the honor of the New England States." The duel was actually a contrived way to assault Cilley who was gaining power in the House of Representatives and posing a political threat to the southern leadership on several hotly contested issues.

On February 24th 1838 the duel was fought on a field a short distance from Washington, D.C. Jonathan went into the duel with the idea that he had nothing against the man whom he was dueling and, because he did not want to cause his opponent any harm, he fired his first round into the ground just ten feet in front of him. The second round missed both men as well. After each of the two rounds, Jonathan's second tried to reach an agreement and call off the duel but Mr. Henry Wise, Graves' Second, would hear nothing of it. Round three proved fatal. Jonathan, shot through the lower abdomen, died of blood loss on the spot. He was only 35 years old. He left a wife and three children, including a daughter, Julia, he had never seen because she was born a month after he had left Thomaston to travel to Washington for the winter session. His sons, Greenleaf and Jonathan Prince (whom the family called Prin or Prinny) were only 9 and 2 years of age. His wife Deborah, a widow at thirty, was to live only another six years.

The U.S. Congress investigated the death and concluded that it was "a brutal political murder". The atmosphere on Capitol Hill was steaming with outrage. The tragedy led to many proposals and finally a bill was passed into law prohibiting the practice of dueling in the country.

In Thomaston, and throughout the states of Maine and New Hampshire, the name of Jonathan Cilley evokes mixed feelings of great pride and deep sadness, even now, more than a century and a half after his death.

Remembered, as well, are his children. Greenleaf went to sea at age 14 and distinguished himself in the Navy and afterwards in his private life. Prin followed closely in his father's footsteps, graduating from Bowdoin College, becoming a lawyer and eventually serving in the Maine Senate. At the outbreak of the Civil War, he was the first man to volunteer for the Maine Cavalry and served as the commanding officer of Company B. He was wounded three times during the war, the first time so seriously that he was not expected to survive. But each time he returned to his troops. Prin eventually rose to the rank of brevet major general by the end of the conflict.

Julia married the son of her mother's best friend, after whom she was named. She raised three sons. Unfortunately, her husband died after only eleven years of marriage.

The Thomaston Historical Society has recently been given, on permanent loan, the Cilley family papers. The collection includes more than 500 letters, several dozen legal accounts and other Cilley family memorabilia from 1820 to 1867. The papers are open to the public for research purposes and are listed with the Library of Congress.

Thomaston Historical Society is greatly indebted to the families of Jonathan Cilley Tibbitts, Jr., Jonathan "Casey" Tibbitts, and Gregory Tibbitts, the great-grandson and great-great-grandsons of Jonathan Cilley, for their generosity and for the opportunity to transcribe and preserve these valuable artifacts.

Eve Anderson's award winning book, A Breach of Privilege: The Cilley Family Collection 1820-1867, contains transcriptions of  hundreds of family letters and commentary about life in Maine, New Hampshire and Washington, D.C. in early through the mid nineteenth century. It also contains first person accounts of Civil War events. The book can be purchased through the Thomaston Historical Society for $28. It is hard bound, with ribbon page marker, and contains 45 photographs of the family members and historic sites.