The issue of the conflict between evolutionism and creationism is the primary theme of "The Satanic Illusion" and motivates all of the action. A supporting theme is time travel, long a fixture in popular fiction. Without the ability to travel in time, the central characters would be unable to make their observations of different ecosystems in succeeding eras. De Camp deals with one of the conundrums of time travel—Won't killing ancient animals change history?—by saying that changes made far enough back in time will be absorbed by great evolutionary trends, and the effects will disappear long before human beings appear. This underlying idea about the effects of time travel makes evolution inevitably the winner over creationism, which does not offer a similar explanation for how ancient animals may be killed without affecting modern times.

Rivers's time traveling machine cannot move geographically, remaining in the central region of North America. This confines the succession of ecosystems the characters visit to one geographical area, with each successive ecosystem probably deriving from the ecosystem previously visited. This idea that each ecosystem evolved out of the ones previous to it implies that there would be earlier ecosystems than the earliest one the characters choose to visit, extending back in time to the moment when life first arrived in North America.

Another significant theme is a conflict between inquiry to learn and inquiry to prove. Hubert and McMurtrie are open-minded, seeking to learn from what they observe. This quality allows Hubert to develop a roundedness denied to Zahn, and it gives McMurtrie credibility when he shows how Zahn doomed Hubert to death. Hubert and McMurtrie are learners; they develop their conclusions from their observations. On the other hand, Zahn is not interested in learning; he intends to make all evidence fit his already made up conclusion. His attempts at making what he sees fit creationism become increasingly ridiculous as he and his companions travel through time. Such closed-mindedness is not unique to clergymen; scientists have often suffered from it, too, with scientific advances coming in spite of scientific theory, not because of it. In "The Satanic Illusion," forcing evidence to fit predrawn conclusions is antithetical to good science; honest people like Hubert would be prepared to adjust their ideas according to rationally derived evidence, in this case from direct observation, whereas dishonest people would defy the evidence and lie about it. This is not to say that Hubert actually converts his views to evolutionism. Instead, he is shown to be willing to allow for the possibility of evolution based on what he has seen; he allows his mind to be open to new possibilities as he learns. On the other hand, Zahn maintains that the evidence for evolution is a Satanic illusion.