Jonathan Clarke was born in Boston on May 20, 1744, the seventh recorded child of Richard Clarke and Elizabeth Winslow Clarke. He entered a large, affluent household already closely connected to Boston’s Atlantic economy. His father, a Harvard-educated merchant, conducted business with London, Canada, the West Indies, and ports along the North American coast. His mother belonged to the prominent Winslow family. Jonathan’s brothers and sisters included William, Hannah, Elizabeth, Edward, Joseph Lee, Mary, Susanna, Isaac Winslow, Sarah, Lucy, and a younger Richard. The family’s wealth and social position gave its children access to the networks of kinship, credit, information, and patronage that sustained colonial commerce.

Unlike his eldest brother William, whose Harvard education is specifically recorded, Jonathan does not appear in the surviving family summary with a named college. His practical education is more clearly visible in the papers of Richard Clarke and Sons. Account books, tax receipts, and correspondence show him learning and participating in the family trade while still a young man. Letters addressed to Jonathan in 1766 and 1767 connect him with the firm’s overseas and Canadian interests, and the company’s records identify him among those handling accounts and commercial obligations. By his twenties, he was not merely a merchant’s son but an active participant in the family enterprise.

Jonathan’s early adulthood unfolded during the imperial disputes that followed the Seven Years’ War. The Clarke firm imported tea and other commodities on a large scale and initially resisted Boston’s nonimportation movement, placing commercial interest and imperial legality against growing popular pressure. Jonathan traveled to London, where he strengthened the connections on which the firm depended. He was there in 1773 when Parliament enacted the Tea Act. Those established relationships helped Richard Clarke and Sons obtain an East India Company tea agency. Jonathan’s return to Boston late that year marked the end of his commercial apprenticeship and the beginning of the public controversy for which he became best known.