The characters in Motherless Brooklyn are both typical figures from hard-boiled detective fiction and humorous takes on those stereotypes. Frank Minna is a clever criminal who recruits boys from St. Vincent's Home for Boys and turns them into "Minna men," essentially crime apprentices. Frank acts as the father figure the boys never had, providing them with a new sense of belonging in the Brooklyn of the early 1970s. As Lionel explains, "it was Minna who brought me the language, Minna and Court Street that let me speak." Like Lionel, Frank uses cryptic language that drives the narrative. Frank has several catchphrases, including "wheels within wheels," which seems to refer to the "secret systems" governing Brooklyn, but could also allude to various social, psychological, and narrative complexities. Another significant piece of advice Frank gives Lionel is to "tell your story walking," linking storytelling not only to physical journeys but also to the act of moving on. For Frank, sharing one's story means departure; he only forms relationships with those who are unaware of his past. The real mystery of the novel is not just Frank's death but his life story. In Motherless Brooklyn, Frank possesses the hidden knowledge the boys crave: insights into his identity, the true purpose of their work, Brooklyn's secrets, understanding of women, and an awareness of their own worth as seen through his eyes. Frank himself is an enigma, one that Lionel must unravel. Solving the mystery of Frank Minna leads Lionel, albeit indirectly, to uncover the mystery of his own identity. Although Frank redeems the boys, he maintains his authority through secrecy. Ultimately, Frank is afraid to reveal his true self and communicate openly, as shown by his advice to stick with big-chested women because "a woman has to have a certain amount of muffling, you know what I mean? Something between you, in the way of insulation. Otherwise, you're right up against her naked soul." Lionel, in contrast, overcomes this fear through his interactions with other characters in the novel and by sharing his story with us, the readers.

Frank's widow, Julia, resembles a classic hard-boiled detective novel character, akin to a tough-talking dame from a Raymond Chandler story. However, like many others in the narrative, Julia is not what she seems. The finale reveals her true origin as a girl from Nantucket, initially seduced by Gerard and his Eastern philosophy, and later by the books Frank read to her—titles by Spillane, Chandler, and Ross MacDonald. These books shape both her identity and her way of speaking. The Minna men also appear to be drawn from a hard-boiled detective novel. They form an eclectic group, brought together because they stand out, not only from other orphans but from each other as well. Tony fits the mold of the typical second-in-command found in mob fiction and films; Danny is the cool, enigmatic character of ambiguous ethnicity; and Gilbert is the essential bottom-tier thug that every hierarchy needs.

Lionel shares several traits with quintessential hard-boiled heroes like Sam Spade and Philip Marlowe. He is alienated from the surrounding culture, detached, ironic, lawless, and skeptical of authority. While Lionel can solve crimes, he cannot significantly disrupt the criminal conspiracies he uncovers. Like other detectives in hard-boiled fiction, Lionel is an anti-hero grappling with both internal and external demons. Similar to Philip Marlowe and Sam Spade, Lionel represents morality in an amoral world. Narrated in the first-person by an anti-hero, Motherless Brooklyn suggests that the lines between truth and appearance are not as clear-cut as they might initially seem. In a novel where there is a disconnect between the spoken word and its meaning—highlighting the gap within consciousness itself—this division becomes even more pronounced.