The killer in, Sherman Alexie's novel Indian Killer, can be defined in two very different ways. First, the novel within the novel (Jack Wilson's Indian Killer) blatantly states who the killer is: John Smith. That said, the killer in the actual novel (the one written by Alexie) is never named.
Many times throughout the novel the identity of the killer is alluded to. Unfortunately for the reader, each time this happens, the assumed killer is exonerated (in a sense). At two points in the novel, Marie states that the killer can not be an Indian. Given that John Smith is Indian (kidnapped from his Native American home/parents and adopted to a White family), Marie's statement would take Smith out of the list of possible suspects.
In the end, it does not seem to be important who the killer is. Instead, the killer is more important given what he represents (which differs with each critical lens applied to the novel). In one way, the killer can be seen as the manifestation of John Smith's rage.