Jonathan Clarkson Gibbs, II (September 28, 1821 – August 14, 1874) was an American Presbyterian minister who served as Secretary of State and Superintendent of Public Instruction of Florida, and, along with U.S. Congressman Josiah Thomas Walls, was among the most powerful black officeholders in the state during Reconstruction. An African American who served during the Reconstruction era, he was the first black Florida Secretary of State, holding the office over a century prior to the state's second black Secretary of State, Jesse McCrary, who served for five months in 1979.

Gibbs was born free in Philadelphia, Pennsylvania, on September 28, 1821. His father was Reverend Jonathan Gibbs I, a Methodist minister, and his mother, Maria Jackson was a Baptist. Jonathan C. Gibbs II was the oldest of four children born to the couple. He grew up in Philadelphia during a time when the city was rife with anti-black and anti-abolitionist sentiments. Gibbs and his brother, Mifflin Wistar Gibbs, attended the local Free School in Philadelphia.

Though not much is known about the details of his early life, Jonathan Clarkson Gibbs grew up in a Philadelphia, where anti-black riots and violence were quite common. Following the death of his father in April 1831, Gibbs and his brother left the Free School to aid their ailing mother and earn a living. The young Gibbs apprenticed to a carpenter. Both brothers eventually converted to Presbyterianism. Gibbs so impressed the Presbyterian assembly that it provided financial backing for him to attend Kimball Union Academy in Meriden, New Hampshire.

Gibbs attended Kimball Union Academy (KUA) at Meriden, New Hampshire, and graduated in 1848. At the time, the academy was under the guidance of an abolitionist principal, Cyrus Smith Richards, who had earlier allowed Augustus Washington (who would also attend Dartmouth) to study at the academy. Washington is best known for a famous daguerreotype of John Brown. At KUA, Gibbs became acquainted with Charles Barrett, a native of Grafton, Vermont, who would become one of his closest friends. The two went on to Dartmouth College, and, later, Barrett returned to his native Vermont and served in politics.

While Gibbs was a student, Dartmouth was under the presidency of pro-slavery Nathan Lord. Lord was originally an anti-slavery advocate who had voted for the Liberty Party and had written editorials in The Liberator. His sudden conversion was due to his conservative brand of Calvinism; he felt that reformers may have been going too far in their zeal against slavery. Notwithstanding Lord's views regarding slavery, which stemmed in large part from his belief that the institution was predicated on sin, he permitted several African Americans to attend the college. Lord believed that any group of people who sinned against God could be enslaved (including whites).

While at the college, Gibbs was influenced by three professors who would affect his thinking as a missionary, educator and politician. He was a member of the abolitionist movement while a college student, and participated in several conventions, appearing by name in The Liberator.

He was the third African American to graduate from Dartmouth College. Following John Brown Russwurm, Gibbs became the second black man in the nation to deliver a commencement address at a college.

Following his graduation in 1852, Gibbs studied at Princeton Theological Seminary from 1853 to 1854, but he did not graduate due to financial constraints. At the seminary, Gibbs studied under Charles Hodge, a pro-slavery advocate. Hodge, a Presbyterian minister, espoused the belief that "slavery as such was not condemned by Scripture but that the way it was practiced in the South perpetuated great evil." Unlike Nathan Lord, Hodge did support the war effort and President Abraham Lincoln. Though Gibbs was unable to graduate from the seminary, he was ordained in 1856. He was called as a pastor of Liberty Street Presbyterian Church in Troy, New York, where Henry Highland Garnet had been pastor. Gibbs invited the pro-slavery president of Dartmouth College, Nathan Lord, to give the ordination sermon. He "begged Dr. Lord as a special favor to preach his ordination sermon, giving as a reason that his college was the only (one) which would endure his presence." Lord delivered the sermon as a result of the absence of other ministers.