Perhaps the biggest and most important theme in The Orchid Thief is obsession. This is what drives Laroche and his orchid lovers to search for the rarest, most lucrative species of flowers. Some might say that obsession is Laroche's defining characteristic. In his life, he has been obsessed with turtles, Ice Age fossils, old mirrors, plants, and, finally, computers. His obsessions are all-consuming: when Laroche loves something, his life revolves around it, and when he falls out of love, he removes that thing from his life forever. This kind of obsession is extreme, but can be found throughout the plant world and, indeed, in Susan Orlean herself. Her quest to see the ghost orchid is a kind of obsession, though she never achieves that goal.

Horticulture is a major theme in The Orchid Thief. It fuels John Laroche's obsession and even gives the book its title. Orchids—in particular, the rare ghost orchids—are the primary focus of the book, but there are many other plants grown by the horticulturists in this book. Bromeliads, sawgrass, and various forms of trees also make an appearance. Laroche himself grew a strain of marijuana that he claimed to have no chemical component, meaning that it could not get a person high. Many people in the plant world are driven by a mixture of love, obsession, and the desire to strike it rich with an especially virile and beautiful plant. In effect, horticulture becomes their way of life.

It is no surprise that the theme of money runs throughout The Orchid Thief. Money is the reason that Laroche tries to steal plants from the Fakahatchee Strand in the first place—his plan was to clone the ghost orchid and make it possible for anyone to grow them at home, thus opening sales of the ghost orchid to the public and making himself a large profit. Millions, he hoped. His desire to make millions may be more overt than that of the other plant dealers Susan Orlean meets, but it's an essential part of the plant world. Everything dealers do—cross-breeding plants, going to shows and conventions, and entering competitions—is geared toward one goal: finding that one plant that will make them rich.

Susan Orlean describes Laroche as "the most moral amoral person [she'd] ever known." By that, she means that Laroche made a habit of breaking the law but having halfway noble reasons for doing so. For example, when he sold his guide to growing marijuana, he did so knowing that the plants people would grow with his guide would be ineffective, meaning they wouldn't have any narcotic effect. In certain lights, his plan to steal plants from the Fakahatchee also had a noble goal: he wanted to take advantage of the loophole in the law in order to expose it—and, hopefully, close it. Though Laroche has what he considers legitimate reasons for breaking the law, he's still a criminal.