We'll start with the obvious: The title Chains refers to slavery. From there, though, it gets a little more complicated, because there's a ton of different kinds of slavery going on in this book. There's the literal enslavement of black people by the colonists, which renders Isabel an object and a possession instead of a human being and allows her to be bought, sold, and beaten against her will. There's also the figurative slavery of the Colonies to Great Britain, keeping them subordinate to the mother country in spite of a growing desire to seek their independence.
Ultimately, the title unites both of these types of chains to capture Isabel's unique experience as a slave at the time of the Revolution. After being rejected for her service by both the American and British armies, Isabel comes to one pretty hopeless conclusion:
I was chained between two nations. (29.50)
Isabel's identity as a slave renders her powerless in the face of the Revolution—she's even expected to automatically assume her master's political convictions rather than develop her own. As a result, a major conflict in Chains is Isabel's bondage between the two sides of the war. She is one stuck girl, and though the title doesn't clue us into it, as the book ends, she's finally breaking free.