Throughout the novel, the motif of a "Heart of Darkness" recurs in Marlow's narration. The first proper mention, although both "hearts" and "dark[ness]" appear earlier, is in Chapter 2, when he overhears a conversation between the Manager and his uncle:
...the profound darkness of its heart.
Later, he cites the title properly, explaining his emotional reaction to the jungle:
We penetrated deeper and deeper into the heart of darkness. It was very quiet there.
(Conrad, Heart of Darkness, eNotes eText)
Although there is no literal "heart" or center of the jungle where darkness can be found, Marlow discovers a sort-of literal "heart of darkness" in Kurtz, who is so damaged by his own hubris and ego that he believes himself a god above the native people. In Kurtz, Marlow sees the capacity of every man to become a dictator if given the opportunity, and so recognizes the "dark" potential in his own heart. Essentially, the title refers both to the "dark," or bad, acts that Kurtz has committed in the "heart," or center, of the jungle, and to the potential in all men to justify cruelty if left to their own devices.