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.