Specifically, Melville criticizes the discipline of ship life and the harsh conditions under which he must live at sea, as well as the attempts of Europeans and missionaries to "civilize" the islanders by destroying their culture. Melville's view is that these influences corrupt the islanders and undermine their native sense of justice and morality, which he finds more appealing than European morality. One example of this is Dolly's first encounter with the islanders on arriving at Nuka Hiva: scores of young women swim out to meet the ship and enthusiastically clamber over the side, naked except for their streaming hair. The unselfconscious manner of these women, their frank sexuality, and their joy at meeting the whalers stand in stark contrast to the social constraints Europeans impose on themselves.

Tommo's decision to make his voyage was in large part fueled by a desire to see what life in the islands was like, and the notion that island life would be a way of "finding himself." In another sense, this impulse is a way of exploring the true nature of freedom by abandoning the rules of "civilization" and embracing a foreign culture.

Tommo's friendship with Toby, who "runs away" with him, is a key element of the book. Like Tommo, Toby also is someone who comes from a higher social class than most sailors; the two men are drawn to each other in part because of this commonality and in part because of Tommo's understanding of Toby's taciturn nature. There is also a certain forbidden quality to their relationship. They are both outsiders to the whaling culture, and their escape to the island is an expression of their transgressive relationship. There is also a hint of sexual attraction between the two, which connects to the notion of the island a sense of sexual freedom.

Much of the suspense of the book comes from the Marquesans' reputation for cannibalism and double dealing. Tommo's suspicions about his ultimate fate underline the difference between his engrained "Europeaness" and the native culture he becomes a part of. This difference is affirmed, of course, by his decision to leave the island, but also by his fascination with tattooing and his fear of being tattooed himself.