Xenogenesis explores some of the problems of human intelligence and how we might overcome them. Though intelligence is a trait that has helped humans survive, humans have warped their intelligence by using it toward maladaptive ends. This has created certain problems within human society and has limited humans' ability to further evolve. These problems include: the human tendency toward racism and xenophobia, our hierarchical social structure, and our reluctance to change. The alien race, the Oankali, provide an outsider's prospective on these problems. They help us see that these limitations, while deeply entrenched, can be lifted. Humanity can choose to use its intelligence in a manner that is more socially harmonious. Indeed, things may have to change if humanity is to survive and continue into the future.

The Oankali often point out that humanity's traits can lead to self-destruction. Jdayah, an Oankali friend of Lilith's, tells her: “You have a mismatched pair of genetic characteristics. Either alone would have been useful, would have aided the survival of your species. But the two together are lethal. It was only a matter of time before they destroyed you.” These two traits are intelligence and social hierarchy. Indeed, it is hinted that humanity's hierarchical social structure has already caused its near-destruction once, in a massive extinction-level nuclear war.

The problems of intelligence are many. Intelligent beings can trick themselves and hide information from themselves. It takes Lilith months to come to terms with her new reality, partly because she is deep in denial. Such strong denial is made possible by human intelligence, which allows us to manipulate and question the facts. However, denial does not serve humanity's continued evolution. The Oankali have settled planet Earth. The old world is gone and in order to survive in this new world, Lilith and the other humans have to face their new reality as soon as possible, and adjust their behavior to this new set of circumstances.

The new situation requires that the humans lean into their other traits: curiosity, adaptability, and flexibility. Lilith is successful because she leans into those traits more often than she succumbs to xenophobia and rigidity: “She had learned to keep her sanity by accepting things as she found them, adapting herself to new circumstances by putting aside the old ones whose memories might overwhelm her.” This adaptability allows Lilith to become close with the Oankali and eventually procreate with them. Lilith personifies the positive traits of humanity. She uses her intelligence in a manner that is flexible and open.

Ultimately, Xenogenesis can be read as a positive take on the possibilities of human nature. Indeed, the Oankali consider humans to be “beautiful. Biologically interesting, attractive . . . fascinating.” The Oankali are intensely attracted to the human race for our capacity to love despite our deep flaws. As one member of the alien race notes: “You are horror and beauty in rare combination. In a very real way, you've captured us, and we can't escape.”