One primary theme is the dichotomy between innocence and sin. This is hinted at by the title of the novel, as "Paradise," in the Christian tradition, is generally a place one can access after death if one is innocent and free from sin. While these ends of the spectrum (i.e., innocence and sin) may not be as clear in real life as their biblical originals, Toni Morrison uses these themes to distinguish between the aspirations (and practices) of town residents and convent residents.
In addition, Morrison uses the allied themes of racial and gender inequality to examine the large issue of social justice. The male rulership in Ruby that is destroying the town, even as they claim its racial superiority and social order, is contrasted to the female sanctuary that the men find intolerable and are thus compelled to punish.
Overall, hypocrisy is a theme underlying the action of this book, combined with the harmful effects of self-delusion. Unable to face the truth, the men seek scapegoats to take the blame for the negative effects of their own myopia, as they deliberately ignore the crisis gripping their town and way of life.
One of the themes in Paradise by Toni Morrison relates to the title of the novel, a novel about different perspectives of what constitutes safety and safe harbor. For one group of people, safety and safe harbor (or paradise) is what for another group of people constitutes a threat to their way of life and existence. In Morrison's Paradise, the only apparent resolution to this dilemma of conflicting points of view upon what constitutes safety is egregious violence.
One theme that Morrison is presenting, a theme that may in itself be as controversial as the points of view presented within her novel, is that paradise has to be fought for--safe harbor can only be won through fighting opponents, as there will always be opponents to one's version of, one's view of paradise--first to gain paradise and then to protect and keep paradise. Another theme is that the attainment of paradise, of one's safe harbor (for which one must paradoxically submit one's self to the unsafety of unending violent fighting) requires at least a periodic suspension of logic and reason and at least a periodic confidence in mysticism and illogicality.