The concept of punctuated equilibrium (PE) had three significant impacts on evolutionary thinking. The first was on the history of biological thought: the critique of a strict phyletic gradualism in paleontology and paleo-anthropology. The second was the theoretical impact for an extension and revision of the neo-Darwinian structure of the theory of evolution, although the organism-centered “Extended Evolutionary Synthesis” shows its blindness in considering the role of macroevolutionary patterns. The acknowledgment not only of the validity of the theory but also of its empirical fecundity is still weakened in philosophy of biology by intentional misrepresentations: for example, the inappropriate conflation of PE with Saltationism. PE concerns both the patterns and the processes of evolution, not only the time but also the mode of speciation. After 50 years of updating, a review of the scientific literature clearly shows that PE has introduced a pluralist view on the rhythms and modes of speciation. The most recent phylogenetic research (integrating molecular, paleontological, morphological data) assigns a central role to “punctuations,” with the possibility to calculate their relative frequency group by group. In paleoanthropology, the complex hominin phylogeny—up to the branching diversification of the genus Homo and cohabitation of different recent human species—can find some clarification in the light of allopatric speciations and biogeographic factors. PE has given an essential contribution in the recognition of the branching feature of the hominin phylogeny against any scenario of progressive hominization.