The American Naturalist recently passed its sesquicentennial. Throughout this long history, it regularly encountered moments of introspection and debate over its goals, mission, identity and audience. Here, we chronicle the history of those debates and transitions at critical moments. The Naturalist began as a popular magazine for amateur naturalists in the late 1860’s. In the late 1870’s it transitioned to an increasingly academic journal for professional scientists, from all branches of the natural sciences. By the turn of the century, academic specialization led to increasing fragmentation of the sciences into a multitude of societies and journals, creating an identity crisis for the once broad-reaching American Naturalist. This identity crisis was resolved when the journal pivoted around 1910 to focus on fundamental advances in the newly-emerging field of genetics. In the 1960’s the journal underwent a remarkably rapid transition to its present focus on evolution and ecology. The profound shifts in the journal’s contents over this time are a reflection of the historical changes in science as a whole: from amateur naturalists, to polymath professionals, to increasingly specialized academics. This chronicle reveals the ways in which the American Naturalist has left its mark on many disciplines, many of which are today only loosely affiliated with the journal, if at all.