[1] Chapman was born in Southampton, Massachusetts, the youngest of five children.

He moved to Georgia and then Florida where he held various teaching positions, and he married Mary Ann Hancock in 1839.

In the early 1840s, he received a medical education, acquiring his MD in 1846.

In 1847, he settled in Apalachicola, Florida, remaining there for the rest of his life working as a physician and botanist, collaborating with Asa Gray.

Working in near isolation, in his spare time, he had a manuscript by 1859 and visited Harvard University for five months, consulting with Gray and arranging for publication of his Flora of the Southern United States, which occurred in 1860.