1. Prothero, D.R., and R.M. Schoch (eds.), 1989, The Evolution of Perissodactyls. Oxford Univ. Press, New York, 537 pp.
2. Prothero, D.R., 1990. Interpreting the Stratigraphic Record. W.H. Freeman, New York, 410 pp.
3. Prothero, D.R., and W.A. Berggren (eds.), 1992, Eocene-Oligocene Climatic and Biotic Evolution. Princeton Univ. Press, Princeton, N.J., 568 pp.
4. Dott, R.H.,Jr., and Prothero, D.R., 1994, Evolution of the Earth (5th ed.), McGraw-Hill, New York, 570 pp.
5. Prothero, D.R., 1994, The Eocene-Oligocene Transition: Paradise Lost. Columbia Univ. Press, New York, 291 pp.
6. Prothero, D.R., and R.M. Schoch (eds.), 1994, Major Features of Vertebrate Evolution. Paleontological Society Short Courses in Paleontology, no. 7, 270 pp.
7. Prothero, D.R., and R.J. Emry (eds.), 1996, The Terrestrial Eocene-Oligocene Transition in North America, Cambridge Univ. Press, New York, 688 pp.
8. Prothero, D.R., and F. Schwab, 1996, Sedimentary Geology. (1st ed.). W.H. Freeman, New York, 574 pp.
9. Prothero, D.R., 1998, Bringing Fossils to Life: An Introduction to Paleobiology, (1st ed.) WCB/McGraw-Hill, New York, 480 pp.
10. Prothero, D.R. (ed.), 2001, Modern and Ancient Barrier, Lagoonal, and Marine Environments, Ventura County, California. Pacific Section SEPM Special Publication 90, 57 pp.
11. Prothero, D.R., and R.H. Dott, Jr., 2001, Evolution of the Earth (6th ed.), McGraw-Hill, New York, 570 pp.
12. Marshak, S., and Prothero, D.R., 2001, Earth: Portrait of a Planet. W.W. Norton, New York, 735 pp.
13. Prothero, D.R. (ed.), 2001, Magnetic Stratigraphy of the Pacific Coast Cenozoic. Pacific Section SEPM Special Publication 91, 394 pp.
14. Prothero, D.R., and R.M. Schoch, 2002, Horns, Tusks, and Flippers: The Evolution of Hoofed Mammals. Johns Hopkins University Press, Baltimore, 309 pp.
15. Prothero, D.R., L.C. Ivany, and E.A. Nesbitt (eds.), 2003, From Greenhouse to Icehouse: The Marine Eocene-Oligocene Transition. Columbia Univ. Press, New York , 541 pp.
16. Prothero, D.R., 2003, Bringing Fossils to Life: An Introduction to Paleobiology (2nd ed.). WCB/McGraw-Hill, New York, 503 pp.
17. Prothero, D.R. and R.H. Dott, Jr., 2003, Evolution of the Earth (7th ed.), McGraw-Hill, New York, 524 pp.
18. Prothero, D.R. and F. Schwab, 2003, Sedimentary Geology. (2nd ed.). W.H. Freeman, New York , 557 pp.
19. Prothero, D.R., 2005. The Evolution of North American Rhinoceroses. Cambridge Univ. Press, Cambridge, 218 pp.
20. Prothero, D.R., 2006. After the Dinosaurs: The Age of Mammals. Indiana University Press, Bloomington, 362 pp.
21. Prothero, D.R. 2007. Evolution: What the Fossils Say and Why it Matters. Columbia University Press, New York, 381 pp.
22. Prothero, D.R., and S. Foss (eds.) 2007. The Evolution of Artiodactyls. Johns Hopkins Univ. Press, Baltimore, MD, 361 pp.
23. Lucas, S.G., Morgan, G.S., Spielmann, J.A., and Prothero, D.R. (eds). 2008. Neogene Mammals. New Mexico Museum of Natural History and Science Bulletin 44.
24. Prothero, D.R. 2009. Greenhouse of the Dinosaurs. Columbia Univ. Press, New York.
25. Prothero, D.R., and R.H Dott, Jr. 2009. Evolution of the Earth (8th ed.), McGraw-Hill, New York.
26. Prothero, D.R. 2011. Catastrophes! Johns Hopkins University Press, Baltimore, 326 pp.
27. Prothero, 2012. A Skeptic's Guide to Global Climate Change. Skeptic Society, Altadena, CA, 28 pp.
28. Prothero, D.R. 2012. Rhinoceros Giants: The Paleobiology of Indricotheres. Indiana University Press, 141 pp.
29. Prothero, D.R. 2013. Reality Check: How Science Deniers Threaten Our Future. Indiana University Press, Bloomington, IN, 370 pp.
30. Prothero, D.R., 2013, Bringing Fossils to Life: An Introduction to Paleobiology (3rd ed.). Columbia Univ. Press, New York, 704 pp.
31. Prothero, D.R. and F. Schwab, 2013, Sedimentary Geology. (3rd ed.). W.H. Freeman, New York, 592 pp.
32. Loxton, D., and D.R. Prothero. 2013. Abominable Science: The Origin of Yeti, Nessie, and Other Cryptids. Columbia Univ. Press, New York, 430 pp.
33. Prothero, D.R., 2015, A History of Life in Twenty-Five Fossils, Columbia University Press, New York, 389 pp.
34. Prothero, D.R. 2016. Giants of the Lost World. Smithsonian Books, Washington, D.C., 174 pp.
35. Prothero, D.R. 2016. The Princeton Field Guide to Prehistoric Mammals. Princeton University Press, Princeton, NJ, 240 pp.
36. Prothero, D.R, 2016, California’s Amazing Geology. CRC/Taylor & Francis, Boca Raton, FL, 470 pp.
37. Prothero, D.R., and T. Callahan. 2017. UFOs, Chemtrails, and Aliens: What Science Says. Indiana University Press, Bloomington, IN (in press)
38. Prothero, D.R., 2017, Fantastic Fossils! A Paleontologist’s Companion. Johns Hopkins University Press, Baltimore, MD (in press)
39. Prothero, D.R., 2017, The Evolving Earth. Oxford University Press, Oxford (in press)
40. Prothero, D.R. 2017, Evolution: What the Fossils Say and Why it Matters (2nd ed.). Columbia University Press, New York (in press)
41. Prothero, D.R., 2017, The Story of the Earth in 25 Rocks. Columbia University Press, New York (in press)