Stephen Jay Gould made impressive contributions to macroevolutionary theory; one of the topics in this area that particularly interested him was how to define and recognize species selection. Here we explore how and why Gould's ideas on concepts related to species selection evolved over 30 years, from the punctuated equilibria paper of 1972 to his “Structure of Evolutionary Theory” magnum opus published in 2002. Throughout his career his ideas on species selection shifted between three phases. Initially, Gould favored a definition of species selection that was more descriptive. Later, he came to distinguish between species sorting, which he called species selection in the broad sense, and true species selection, which is tied to the concept of species-level aptations. Finally, he came to view species selection in a broader, more inclusive way, effectively merging the two earlier viewpoints. His ideas on species selection changed over the years because he was trying to square his views on complex concepts like adaptation, natural selection, emergence, and the independence of macroevolutionary theory. Gould's thoughts on species selection not only help to define the history of debate on the concept but also help set a course for the future.