Identity
Identity is one of the main themes that is explored greatly in the novel, largely through the titular character Little Tree himself as he seeks out his personal identity. We mainly see the conflict between his identities as a native american Cherokee and as a white american. Given his unique lineage, he is tormented in school and through his struggles, we are able to better understand how these conflicting identities ties in together to make up who he is.
Love
The novel mainly focuses on familial love. Given that Little Tree's parents died when he was just a toddler, we see how his grandfather takes the place of the father figure in Little Tree's life. We are also able to observe how Little Tree's relationship with his family develops through his experiences as well as in the later deaths of both his grandparents before he turns ten.
Religion
Religion also plays a minor part in the novel and we see many differing viewpoints on the issue in the novel. These come into conflict and have a profound impact on Little Tree's development and growth as a young boy. Due to the numerous Christian denominations that worship in the town, there are frequent arguments about the Bible and this leaves Little Tree and his grandparents both confused and skeptical about religion.