Ferdinand Lindheimer is credited with the discovery of hundreds of plant species and it is estimated that he collected as many as 100,000 plant specimens during his lifetime. Many plant species today use Lindheimer's name as a designation in their scientific name, such as Lindheimer's Morning Glory (Ipomoea lindhimeri), Texas Yellow Star (Lindheimera texana), and Lindheimer Muhly Grass (Muhlenbergia lindheimeri).

Ferdinand Lindheimer made an agreement with fellow botanist George Engelmann to collect and send Texas plant samples for categorization. The agreement included shipments to Asa Gray at Harvard College. For each sample he collected, Lindheimer recorded the date, location, habitat, and general characteristics. He also pressed and dried the plants before sending them to Engelmann and Gray.