Jon Edward Ahlquist (27 July 1944 –7 May 2020) was an American molecular biologist and ornithologist who has specialized in molecular phylogenetics. He has collaborated extensively with Charles Sibley, primarily at Yale University. By 1987, both Ahlquist and Sibley had left Yale. In 1988, Ahlquist and Sibley were awarded the Daniel Giraud Elliot Medal by the National Academy of Sciences. In January 1991 (often listed as 1990), Charles Sibley and Ahlquist published Phylogeny and Classification of Birds, which presented a new phylogeny for birds based on DNA-DNA hybridisation techniques, known as the Sibley-Ahlquist taxonomy. At that time, he was an associate professor of zoology at Ohio University. In 1999, Ahlquist was retired.
- Theodore W. Pietsch (2012) Trees of Life: A Visual History of Evolution. Johns Hopkins University Press. p. 275
- Jon Edward Ahlquist obituary, The Huntsville Times, 9–10 May 2020.
- "Daniel Giraud Elliot Medal". National Academy of Sciences. Archived from the original on 20 June 2014. Retrieved 15 June 2014.
- Ahlquist, Jon E. (1999). "Charles G. Sibley: A commentary on 30 years of collaboration". The Auk. 116 (3): 856–860. doi:10.2307/4089352. JSTOR 4089352.