The Chrysalids is a strong cautionary tale about the danger of religious doctrine and eugenics.
Wyndam was highly influenced by events happening before he wrote the novel, especially World War II. During the war, he worked for the Ministry of Information and then as a corporal in the army working with codes. Wyndam would have been heavily influenced by the eugenic race-purifying movements of the Nazis and the threat of nuclear annihilation once the US dropped an atomic bomb in Japan.
In The Chrysalids, a post-apocalyptic world has left humans in the hands of religious fanatics. Anyone who does not look a certain way is expelled, and any animals that don’t conform to specific requirements are killed.
An example of the way the language used is very similar to Nazi policy is when the inspector lectures David on why he needs to turn in his friend Sophie for having six toes.
'Loyalty is a great virtue, but there is such a thing as misplaced loyalty. One day you will understand the importance of a greater loyalty. The Purity of the Race -- ' (ch 6)
Besides the damage of religion, there is the potential for danger in any totalitarian arrangement, especially when a group tries to make people conform.