Stephen Jay Gould cited Prothero's research on the lack of response to climate change in mammals from the Eocene, Oligocene and Pleistocene epochs to support the punctuated equilibrium model of evolution.

The magnetic reversals are precisely dated and consistent worldwide which allows these rocks to be studied in climate science and evolution.

[9] Prothero's work on documenting evolutionary history of fossil vertebrates was cited by Richard Dawkins in his book The Greatest Show on Earth: the Evidence of Evolution.

[18] In October 2012, Prothero appeared in his capacity as a paleontologist on Conspiracy Road Trip, a BBC television documentary in which five individuals who self-identified as Creationists participated in a road trip along the western coast of the United States, meeting with various experts on the topic, exchanging views and questions with people holding differing views.

[19] Prothero has frequently written about the topic of cryptozoology, a pseudoscience and subculture, which he categorizes along with Holocaust denial and UFO abductions claims as aspects of American culture that are "clearly baloney".

[20] Prothero's 2013 book with Daniel Loxton, Abominable Science: The Origin of Yeti, Nessie, and Other Cryptids discusses the subculture in depth.

In a review by Adrienne Mayor of Stanford University, she describes the book as "An entertaining, educational, passionate, and valuable handbook for readers interested getting a scientific perspective on the field of cryptozoology.

We have a good understanding of how and why the Antarctic ice sheet first appeared at that time, and how the Arctic froze over about 3.5 million years ago, beginning the 24 glacial and interglacial episodes of the 'Ice Ages' that have occurred since then."

[33] While the reviewer praised Prothero for his approach to these topics and "recommended" the work, Prothero's "presentation becomes more complex" as the book discusses ice ages and global warming according to the reviewer, who states that "with all scientists convinced that warming is occurring as a result of human action, [...] he disparages the denialists.

[34] His book Evolution: What the Fossils Say and Why it Matters received the 2007 PSP award for excellence in earth science from the Association of American Publishers.

[35] In 2013 he received the Diamond Award for Distinguished Achievement in Science and Technology from the Glendale Unified School District.

"[39] The Committee for Skeptical Inquiry (CSI) awarded Tim Callahan and Prothero the Robert P. Balles Annual Prize in Critical Thinking for their book UFOs, Chemtrails, and Aliens.