A good overview of The Chrysalids may be found here. Some themes prevalent in the novel include:
1. Isolation and Alienation: David and the "abberrations" are considered as outcasts and alienated from Waknuk's society.
2. Religious persecution
4. Salem on Literature says "The Chrysalids proposes that ignorant adherence to the “word,” or to religious tenets, has dehumanized the world, and that only in transcendence of past beliefs will humanity resurrect itself. The message is distinct: People must throw off the mind-forged chains of the past, bury fears and prejudices, and walk as one with enlightened steps into the future, or else stumble and perish forever."
5. Life in a post-apocalyptic world.