Sexism
Mary Conant, the main character of the novel, begins as the perfect mold of a nineteenth century women in the town of Salem. However, she soon finds that the sexist attitudes of her male counterparts are quite intrusive, as well as hard to live by. Beginning with her father, she slowly drifts away from the men in her life, and denies the role that she was supposed to play as a woman. She neither allows herself to be controlled by men or religion, and pursues Charles Brown and Hobomok as potential husbands, despite her father's request.
Religion
Growing up strictly Puritan, Mary was told that she had to fit into society and remain a pure woman. But, Mary is not the only one in the town of Salem being told to stay in her place by the Church. In fact, Mr. Oldham, one of the townspeople, composed a letter explaining to the Church that, if it continued to repress people, then there eventually would be some sort of rebellion. Although we do not see that in this novel, Mary and the other townspeople grow further away from the Church, which disapproves with the ways of Native Americans. Seeing how kind most of the Native Americans actually are, the townspeople think the Church may not be as "Pure" as it claims to be.