The title of this excellent story itself yield what is, to me, the central theme. By choosing a title including the word "Chrysalids," Wyndham points towards the way in which humanity is changing and developing, moving from its caterpillar state into something new. Of course, the fact that the title includes the words "chrysalids" indicates that this transformation and change is not completely over yet, and thus we are plunged into the frightening world of David and Rosalind and their companions, who recognise that they are different from the rest of the humans they live with, but must hide those differences.
The focus on transformation and evolution is likewise signalled by the woman from Sea Land, who states clearly that "life is change" and "The living form defies evolution at its peril; if it does not adapt, it will be broken." Thus the central theme of the novel points towards the way in which humanity is constantly changing and evolving and how we must embrace that.
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One theme in the Chrysalids is discrimination. We can see discrimination against deviants throughout the book. The rules set by Nicholson are discriminatory towards deviants and the practices of people (Like Joseph Strorm) are very discriminative. They banish those who do not look like the True Image of God and they eradicate Offences. We can see the harsh and unjust treatment deviants receive just because they appear to look abnormal.
The Chrysalids is a novel based on discrimination against deviants and we can see a number of cases where this takes place. For example, Sophie's incident, shunning of Aunt Harriet for coming up with an idea to protect her deviated newborn, David and his fellow telepaths and all the other Fringes people.