Any time you read a piece of writing (literature) you should ask yourself this question:
"What is this piece about?" Then go with your gut and fill in the blank.
This piece is a (story/poem/essay/novel) about_____________. Love, isolation, greed, reality vs. illusion, good vs. evil, etc.
Whatever you fill in the blank with is one of the themes. Most pieces have more than one, especially if it is well-developed and pays attention to detail. Take Shakespeare, for instance. His plays have 100's of themes all at once.
As long as you can point to examples from the beginning, middle, and end of the story to support the idea you've placed in the blank, you can be certain that your gut reaction is correct as a theme.
This book has two overriding themes. One theme is the importance of handling and taking care of horses properly. The eNotes discussion of this book's theme states that
Horses that are treated with respect and compassion turn out well; those who are abused, intentionally or unintentionally, turn out poorly. This theme is introduced when the narrator contests the popular belief that in "breaking" horses "the cowboy breaks the horses' spirit." The narrator goes on to assert that "breaking a horse the way he's broke on the range is about the same on the animal as schooling is to the human youngster."
The friendship between Clint and Smoky is the other theme. Enotes remarks: "The value and intensity of Smoky and Clint's friendship are vividly illustrated when Smoky brings the injured Clint home and when Clint undertakes a painstaking search for the missing Smoky, eventually rescuing and rehabilitating him."
Walt Disney made a movie about Smoky in the 1960s, emphasizing the special bond between the man and his horse.