Obsessive Love
The theme of obsessive love drives much of the plot of the novel and lies at the heart of Elio's development as a character. Elio becomes obsessed with Oliver's body, mannerisms, and relationships. He frequently fantasizes about and longs for physical intimacy with Oliver, shown in his dreams and in his incessant thoughts of Oliver, which he struggles to conceal from Oliver and the other residents of the villa.
Such love is shown to take control of a person's thoughts and leave a permanent imprint on the lover's memory once the love is consummated. It is a force greater than oneself, pulling the lover toward their object of desire inextricably. Elio's obsession evolves from infatuation to romantic love to a love that ultimately punctuates his life story and goes on to influence his perception of love forevermore.
Friendship
In the relationship between Elio and Oliver, friendship is just as important as their passion and sexual desire. Elio desires not only physical intimacy, but also friendship with Oliver, and Oliver reciprocates these feelings. Together, they find a partner with which to talk about anything: literature, philosophy, music, and work.
The theme of friendship also appears in Oliver's close friendship with Vimini, the 10-year-old leukemic genius. Though Elio cannot understand why the two become so close, it seems to him more natural and beautiful than his own friendship with Oliver. Additionally, Elio's relationship with Marzia explores the line between friendship and sexual intimacy.
Elio's parents insist that Elio spend more time with friends, and much of the novel explores Elio's process of understanding "why others are so important," as his parents put it.
Time
Time in the novel is both merciless and eternal, something that both happens to the characters and passes through them. At times, Aciman's prose evokes a feeling of timelessness, and later in Elio's life, his memories of his summer with Oliver possess a timeless quality to them. Memories of the summer blur into one another and the languid routine pastimes at the villa paint large swaths of time with the same brushstroke. Moments that punctuate the summer, such as the episode at Monet's berm, take on this timeless quality as well: they live on in Elio's memory, in Oliver's postcard, and—in a meta-literary sense—in the text itself, forever accessible.
Knowledge of Oliver's limited time at the villa looms over the entire novel. While Elio knows that his time with Oliver is limited, mention of the approaching departure date is seemingly overlooked in favor of a timeless tone, while time continues to pass and challenge Elio's ability to be with Oliver—merciless and eternal at once.
Sexuality
Both Oliver and Elio feel sexual attraction to both men and women. Elio's coming-of-age story is as much a discovery of life-defining love as it is a discovery of his sexuality. As the novel progresses—as his relationship with Oliver deepens and he gains insight into the human nature of desire—he recovers memories of his adolescence in which his attraction towards men begins to manifest.
The novel is remarkable for its treatment of bisexuality in the way that it portrays desire and love as something that transcends sexual preference. Sexual desire is something which several characters in the book experience and ruminate on, but the book portrays this as a unifying quality of the human experience, making no distinction between hetero- or homosexuality.
Heraclitus and Pre-Socratic Philosophy
The novel makes recurrent mention of the pre-Socratic philosopher Heraclitus, whose writing Oliver is studying at the villa. Oliver's own academic expertise is pre-Socratic philosophy, a matter which the family initially finds surprising when they decide to select him as the annual fellow because pre-Socratic philosophy is a rather niche academic subject.
The term 'Pre-Socratics' refers to a number of ancient Greek philosophers predating or contemporary with Socrates of Athens, one of the founders of the western philosophical tradition. Heraclitus, one of the more famous pre-Socratics, lived around the 6th - 5th centuries BCE in Ephesus, then part of the Persian empire. He is renowned for his insistence on change being the fundamental essence of the universe (one of the earliest explorations of the philosophical concept of 'becoming') and stark commitment to a unity of opposites in the world, stating that "the path up and down are one and the same."
Judaism
Elio's mother calls her family "Jews of discretion." While they neither hide nor repress their religious identity in an overwhelmingly Catholic country, they make a point of not outright showing it. Elio grows up insecure about his Jewish identity. When Elio discovers that Oliver wears a Star of David necklace and makes no point of hiding it—even showing it boldly on his chest with his top shirt buttons unbuttoned—he realizes the possibility of being more at ease with this identity. Elio and Oliver also share several moments discussing Paul Celan, the 20th-century Jewish German-language poet. André Aciman's own Jewish background—particularly his experience growing up in a Jewish family in Egypt as a religious minority—influences much of the novel.
Silence
In an interview with Vanity Fair, Aciman states he "couldn’t write silence...what I do is chisel a statue down to its finest, most elusive details." From Oliver's curt farewell, Later!, to Oliver's inability to confess his feelings, those things left unsaid are just as important in the novel as those outright stated. The first half of the novel sees Oliver and Elio exchange concealed flirtatiousness and affection, and even when Elio finally confesses his attraction, he does so indirectly by admitting that there is "something he doesn't know," alluding to Oliver's sexuality and his own feelings toward Elio. Instead of asking Oliver verbally when Elio decides to ask for sexual intimacy, he does so in the form of a note, and even then he avoids the matter directly, stating, "Can't bear the silence. I need to speak to you." Though the love between Elio and Oliver is evident and bold, the words "I love you" are entirely absent from the novel. The pair seems to communicate through silence, indirect reference, and by reading each other's subtle gestures more than they do through explicit mention of their desires.