Sexuality
Both Dante and Ari are exploring their own sexuality and learning about themselves. They are at different stages of their respective journies of self-discovery. Dante knows that he is gay, and has come to terms with that when we first meet him. Although there is some deliberation (he thinks he would like kissing boys more than he likes kissing girls) he is at heart certain that he is attracted to men, and that he is gay, and he is actually very comfortable with that.
Ari is at a far different stage. Prior to meeting Dante, it would never have occurred to him that he might be gay. The moment he meets Dante he is infatuated, and he later admits that he was in love the moment that he set eyes on him. Ari is in denial about his sexuality. He actively seeks out girls to kiss and has a genuine attraction to and crush on Illeana. He also becomes angry within himself when he realizes that he is in love with Dante but he doesn't want to admit it. He even rejects Dante's attempts to kiss him, or to get him to feel something when they eventually do kiss.
Dante's chief concern is how his parents will react to his coming out, and this is also one of the sub-themes within this theme of sexuality. The reaction of those around the boys is studied quite closely, and it turns out that both sets of parents are well aware that the boys are in love with each other before they are told— and, in Ari's case, before he is even prepared to admit it to himself.
Anti-Gay Discrimination
As well as dealing with a theme of sexuality, the novel also has a theme of discrimination against gay people. This is seen both through a violent act against Dante and the quieter ostracization of Ari's aunt Ophelia.
Ophelia has been shunned by all of her family, except for Ari's parents, because she is a lesbian, and because they have discovered that she is living with her female partner. Although the discrimination against her is not physically violent, it is still a scary prospect. Therefore, the fact that Ari's parents are the only ones who continue to accept her makes Ari less afraid about how his parents will react to the news of his homosexuality; they are clearly people who stand up for what they feel is right, and who are accepting, without worrying what the people around them think. They are the opposite of people who discriminate.
Dante is beaten up because of his sexuality. When thugs see him kissing Daniel, they beat him up, purely because of this expression of his sexuality. Dante is prepared to stand up for himself but Daniel does not, and this shows that Daniel is not yet ready to be "out" as a gay man or to be proud of his sexuality.
Isolation
Ari feels isolated from everyone. He is very lonely and he does not have any friends. However, he is also isolated from his family. This is primarily because they are very non-demonstrative people, and they keep their feelings close to their chest. This makes Ari feel very isolated when it comes to certain subjects. For example, he is frustrated about the silence surrounding what has happened to his brother. The family acts as if Bernardo is dead, and they don't explain why. This is a very isolating experience. He is also very isolated socially before he meets Dante, because he does not have any friends.
Family Dynamics
Dante's family is very close and they are very comfortable showing their affection for each other. They frequently say "I love you" and they talk about any issues that arise. This is a stark contrast to Ari's family, which is silently loving but dysfunctional.
There is a lot of love in the Mendoza family, but it is tacit. Everyone plays their cards very close to their chest and consequently, Ari feels like his parents don't know him, and he doesn't know them either. As the novel progresses, his relationship with them deepens and opens up more and he finds that he thinks much more of them as people than he believed he ever would. The main issue in their relationship is the deep denial that, in their own way, each family member engages in.
Ari's father is in denial about what he experienced in Vietnam, and he believes that if he doesn't talk about it to anyone then it didn't really happen. He won't talk to his wife about how he feels and he has never told Ari anything about his time in the war. Ari's mother had a nervous breakdown when his brother was arrested for murder, and was unable to look after Ari for a time. She cannot talk about this because it was such a difficult time and she cannot tell Ari about his brother. The family pretends that he is dead so they don't have to face the reality of his life. However, all of the secrets within the family make it very dysfunctional and it is only when things are brought out into the open that the family dynamics change and improve immeasurably.
Mexican-American Heritage
One of the themes of the book is that of Mexican-American heritage and the way in which both boys interpret their ethnicity. Although there are no incidents of discrimination against them, there are a number of stereotypes dealt with in the book, including gang membership (Illeana's boyfriend is a low-ranking member of a Mexican street gang) and also the traditional view of masculinity and manhood within the Mexican community.
Coming of Age
Much of the book centers around Ari's coming of age as a teenager, moving through all of its awkward physical, mental, and emotional changes. As the novel progresses, both Ari and Dante mature physically and emotionally, and beyond just being about discovering their sexual orientations, Aristotle and Dante is very much a novel about two boys who are on the verge of becoming adults, and what that might mean for them. Ari struggles with what it means to grow up, particularly in the shadow of a brother he has never really known.
Secrets and Telling the Truth
The whole book centers around the secrets people keep from each other and from themselves. Part of Ari's fascination with Dante is that Dante, unlike anyone else in Ari's life, seems incapable of lying to or about himself and incapable of even really keeping secrets. Dante's openness is juxtaposed with the secrets that seem to characterize Ari's family, from his father's struggles in Vietnam to his brother's imprisonment to his own feelings for Dante. Arguably, the most important thing Ari—as well as other characters—learn throughout the course of the text is how to be honest in a variety of ways.
