A chief moral lesson in the novel is that we can soar higher than we think we can and that doing so brings us closer to heaven and the Great Gull, which is God. Then, as we get nearer to God, we become more fully gulls (or whatever species we are), and we realize that love and forgiveness are all-important.

There is no bible verse quoted verbatim in Jonathan Livingston Seagull, but some of Jonathan's utterances echo bible verses. For example, Jonathan tells Fletch that

You have to practice and see . . . the good in every one of them [the other seagulls] and to help them see it in themselves. That's what I mean by love.

This accords with several biblical concepts: first, that creation is good, and second, that love involves seeing and affirming the good in others. Love is all-important both in the Bible and in Jonathan's theology. The Bible tells us to love one another, just as Jonathan tells Fletch to love the other seagulls.

Most simply stated, the moral of the story is "that if one does what he likes and ignores everything else, he will be fulfilled and transcend even death with few problems." There is more that should be considered, however.

Jonathan starts the story appearing to be self-centered and stubborn, focused upon learning how to fly to meet his personal dreams regardless of requests from his family or condemnation from his society. Later, Jonathan comes to understand that his true desire in life is to be an instructor and give truth to other gulls according to his understanding of love:

to be an instructor, and his own way of demonstrating love was to give something of the truth that he had seen to a gull who asked only a chance to see truth for himself.

In some senses, Jonathan Livingston Seagull oversimplifies the conflicts between the challenges of dealing with opposition and ignorance or misunderstanding and being true to oneself and personal destiny. However, the allegories presented can also serve as an inspiration and a hope for what is possible.

While there are parallels between Jonathan and Jesus, the Great Gull and God, there are no direct Biblical verses in the story. Ideas found in other religions besides Christianity are present in the relationships, actions, and suggestions offered throughout the book.