Because of Rothenberg's study of animal song and his experimental interactions with animal music, he is often called an "interspecies musician". According to Andrew Revkin, Rothenberg "explores the sounds of all manner of living things as both an environmental philosopher and jazz musician."
Rothenberg's book Why Birds Sing: A Journey Into the Mystery of Bird Song (2005) was inspired by an impromptu duet in March 2000 with a laughingthrush at the National Aviary in Pittsburgh. In the wild, male and female laughingthrushes sing complex duets, so "jamming" with a human clarinet player was closely related to the bird's natural behavior. A CD accompanying the book also featured Rothenberg's duet with an Australian lyrebird. The book served as the basis for a 2006 BBC documentary of the same name.
Rothenberg's book Thousand Mile Song (2008) reflects similar curiosity about whale sounds considered as music. He seeks out both scientific and artistic insights into the phenomenon. Philip Hoare said of the book, "..while Rothenberg's madcap mission to play jazz to the whales seems as crazy as Captain Ahab's demented hunt for the great White Whale, it is sometimes such obsessions that reveal inner truths...I find myself more than a little sympathetic to the author's faintly bonkers but undoubtedly stimulating intent: to push at the barriers between human history and natural history."
He is currently at work on a book about insects and music, to be published by St Martins Press in 2013, a project he began at the 2006 International Arts Pestival in London. During the 2011 emergence of Brood XIX periodical cicadas, Rothenberg was the subject of a YouTube video as he played saxophone to accompany the mating calls of Magicicada tredecassini.