His grandfather (Pierre Boudouin) was a Huguenot refugee from France. Pierre took his family first to Ireland, then to Portland, Maine, finally settling in Boston in 1690. His father, also James Bowdoin, was a successful merchant in Boston when James was born there on August 8, 1727.
Young James attended Harvard, graduating in 1745. When his father died in 1747, he inherited a considerable fortune. He took an early interest in Natural History, and had several papers read to the Royal Society in London by his friend and correspondent, Benjamin Franklin.
Bowdoin was elected to the colonial assembly in 1753 and served there until named to the Council in 1756. By the end of Sir Francis Bernard's term as governor he spoke and wrote against the royal governors and their actions. He was proposed as a continuing Council member in 1769, but the new governor Thomas Hutchinson rejected his membership. Boston promptly elected him to the assembly. When Hutchinson was formally commissioned as governor in 1760, he restored Bowdoin to the Council, reasoning that he was less dangerous there than as an outspoken critic in the assembly.
Bowdoin as named as a delegate to the Continental Congress in 1774 but did not attend, citing health reasons. In 1775 he was elected President of the Council and held that office until 1777. With the turmoil of the American Revolutionary War, he sometimes acted as council president in an executive, rather than legislative role.
When Massachusetts wrote its own constitution in 1779, he was president of the Convention which created it, and chairman of the committee that drafted it. His son, James Bowdoin III, also sat in this convention. Under the new state government, governor John Hancock appointed him to a commission to revise and consolidate the laws from colonial days.
In 1785, Bowdoin was elected Governor of Massachusetts, but his terms were not peaceful. He called up the militia and took vigorous action to put down Shay's Rebellion, and as a result lost the election of 1787 as Hancock was swept back into office. In 1788 he served as a member of the Massachusetts' convention that ratified the United States Constitution.
Throughout this period, he maintained his interest in learning an natural history. In 1780 he was primarily responsible for the creation of the American Academy of Arts and Sciences, He served as its first president until his death and left the society his library. Bowdoin continued to publish not only scientific papers, but verse in both English and Latin. He was awarded an honorary doctorate by the University of Edinburgh, made a fellow of Harvard, and was a member of the Royal Society of both London and Edinburgh.
He died of consumption on November 6, 1790 in Boston. Bowdoin College in Maine was named in his honor.