The most obvious theme of the novel is guilt. The issues of how much guilt is, or should be, felt; how guilt manifests itself, both internally and externally; and how guilt can be addressed are all explored. Several of the characters, including Macarthur, Claythorne, Armstrong, and even Brent, suffer from a deep sense of guilt. Of course, other characters, including Marston, Lombard, and Wargrave, don't seem to harbor any sense of guilt. As such, the novel suggests that guilt is a very complex and individualized emotion.
Concealment is another main theme of the novel. Obviously, each guest to Indian Island has been able to "largely" conceal his or her involvement in the death of another human being. Of course, the method of concealment varies from guest to guest. For example, Armstrong and Blore rely on fraternal courtesy and the respect afforded to them as professionals. Wargrave utilizes his position of power and authority as a judge. Marston and Macarthur rely on the fact that the deaths related to them were, by definition of the law, accidental. Thomas and Ethel Rogers and Miss Brent hide behind the cloak of inaction. Lombard relies on the fact that he is operating in an uncivilized environment. And Claythorne utilizes the impulsive and irrational nature of youth, as well as love.
But concealment operates on other levels, too. Initially, the guests hide specific details about their lives from one another. At various points in the novel, the characters conceal their true thoughts and feelings. Of course, the island is a geographical manifestation of concealment. It is, in effect, cut off from the mainland. Finally, the storm further conceals the events happening on Indian Island from the rest of the world.
Because the murderer has discovered the truth about each individual, the novel suggests that no matter what method of deceit is employed, the truth can never be fully concealed.
Justice is another of the novel's major themes. Wargrave's letter of confession indicates that he long had a fascination with both death and justice and that he performed the murders as a way of providing justice for crimes the law could not touch. Justice is also explored in other ways, as Brent suggests that Mrs. Rogers' death was God's way of delivering justice. Of course, the entire novel calls into question the issue of justice: are the murders true justice, some sort of retribution, or simply the acts of a sick mind?
A final theme in the novel is that of suspicion. As the guests recognize that Marston, Rogers, and Macarthur were murdered, they begin to suspect each other. Thus, the novel asks what it means to be a suspect and explores the nature of suspicion. This sense of suspicion builds in each character as subsequent murders take place, and eventually transforms into a strong sense of paranoia.