The theme of Jonathan Livingston Seagull by Richard Bach is self-discovery through seeking a higher existence as a nonconforming individual.
Jonathan’s inner conflict of whether to conform to the “sea gull” way of life or to leave that life to take flight plays out through the story. The gull feels there is more to his existence than using his cursory flight abilities to obtain food. He envisions life outside the limits imposed on him by “society.” He wants to soar even at the expense of becoming an outcast from his flock.
Although he falters along the way, through his investigations and travels he realizes the positivity of practice and education. Jonathan is not content with his newfound knowledge and abilities; therefore he returns to his flock to locate and educate other outcasts about the possibilities that exist in life, even if it means loneliness, isolation, deep introspection, and reexamination of common beliefs.
The symbolism of flight and the cliché of “the sky is the limit” play out throughout the book.
Sometimes sticking to your beliefs comes with a great price. Resisitng the current of ideas held to be true or acceptable can make you very unpopular or even bring ridicule and alienation. Going against the crowd can be a lonely road, but if you believe in yourself and your convictions, you are still a 'winner' at heart: "To thine own self be true."
Another theme is that isolation is often necessary for the transmission of knowledge. A leader must often distinguish himself from the crowd before he has any followers or before he can offer a different path from that which is already known.
The overall theme of the book is that we should all strive to reach our greatest potential and break out of the boundaries that limit us. Bach tries to fuse the enlightenment thought that man (or gull) himself can overcome all obstacles with both New Age and Christian concepts of the soul and the afterlife to create his own spiritual philosophy.