One of the main themes of the book is the question of whether the mutiny against Captain Bligh is justified. Bligh is portrayed as a harsh disciplinarian, but he also believes that this type of discipline is necessary on the high seas, far from the reach of law. The practice of flogging that he uses was customary at the time, and the men aboard ships at that time were notoriously difficult to control. In addition, Fletcher Christian is described as a romantic and mercurial leader whose ego is harmed when Bligh accuses him of stealing coconuts. In other words, Christian might have been motivated to plot the revolt in part because he wanted to protect his own ego. While Bligh is not the most likable of men, he is a truly skilled sailor who is able to pilot his launch to safety once the mutineers set him and his men adrift.

Therefore, whether or not the mutiny is justified is left ambiguous. Is Bligh so awful that the men are justified in almost killing him and then overthrowing him, or is he similar to many other harsh sea captains in the English navy at the time who were trying to keep order while on the high seas? The book asks whether it is justified to use force to compel discipline or whether leaders who use force should be justifiably removed.

Another theme in the book is the beauty and freedom of the state of nature. At the beginning of the book, Roger Byam's mother mentions to Captain Bligh that she and her son have been reading the work of Rousseau, who writes about how people are freer in the state of nature and how people's freedom is constrained in society. When Byam gets to Tahiti, he finds the life there idyllic, as the people are living in a state of nature. Tahiti is the embodiment of the ideal that Rousseau writes about, while England, to which Byam is returned literally in chains for his trial for mutiny, does not offer him this freedom. Though Byam is eventually spared, England is for him a land in which, despite its apparent civility, he cannot live in complete freedom as he did in Tahiti.