Alan Templeton's work involves the application of molecular genetic techniques and statistical population genetics to a variety of evolutionary problems, both basic and applied. He applies evolutionary approaches to clinical genetics, including the study of the genetics of coronary artery disease and the evolution of the HIV virus within infected patients. He also applies evolutionary genetics to conservation biology, with his main current focus being the impact of managed forest fires at the landscape level upon the genetic population structure of species inhabiting that landscape. Finally, he is interested in basic questions about evolution, such as the meaning of "species" and the mechanisms by which new species evolve, and recent human evolution.

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A grasshopper, Trimerotropis saxatilis.