The title of the novel may be a reference to various elements within the narrative. Anil's Ghost could refer to Anil's struggle to unify her past in Sri Lanka and America with her present life; it may also refer to Sailor, the skeleton which Anil and Sarath work to identify, and which symbolizes, in a single entity, all the victims of war. It is, in this reading, the destruction of innocent lives that haunts Anil and drives her to identify the victim as well as the culprit who killed him.
Another interpretation could be that it references the "ghosts" of Sri Lankan atrocities that affect everyone Anil meets during her time there. Every character in the book has deep psychological scars from the violence. Finally, the archaeologist Sarath may be Anil's ghost: His sacrifice at the end of the novel lives on as a memory in Anil and others; as such, he lives on as a ghost. Ananda, indeed, refers to "the ghost of Sarath," and how he and Anil will always carry it.