The name Johnathon is derived from the Hebrew name Yonatan, which means "Yahweh has given" or "gift of Yahweh". It is a combination of the Hebrew words "yo" (Yahweh) and "natan" (to give). The name originated in ancient Israel during the biblical period and was first mentioned in the Old Testament.

One of the earliest and most famous figures with this name was Johnathon, the son of King Saul and a close friend of David. Their friendship is celebrated in the biblical Book of Samuel. Johnathon played a pivotal role in supporting David's rise to power and eventual kingship over Israel.

During the Middle Ages, the name Johnathon gained popularity across Europe, particularly in England and Scotland. It was often spelled as "Jonathan" or "Jonathon". In the 12th century, a notable figure named Johnathon the Scribe lived in England and was known for his excellent calligraphy skills.

In the 16th century, Sir Johnathon Trelawny was a prominent English politician and member of Parliament. He was born in 1580 and played a significant role in the English Civil War, supporting the Royalist cause.

The name Johnathon also has a literary connection. In the early 19th century, American author Herman Melville featured a character named Johnathon in his novel "White-Jacket". This helped to further popularize the name in the United States.

Another notable figure was Johnathon Edwards, the famous American Puritan philosopher, preacher, and theologian. He was born in 1703 and is widely regarded as one of the most influential thinkers of the Great Awakening religious movement in colonial America.

Throughout history, the name Johnathon has been associated with individuals known for their intellect, wisdom, and strong moral principles. Its biblical roots and meaning as a "gift from God" have contributed to its enduring popularity across various cultures and religions.