AbstractA number of researchers working on the origin of extant Neotropical biodiversity implicitly and without appropriate proofs assume that Pleistocene speciation should necessarily follow the rules of the refuge hypothesis. A recent example is provided by a study of Neotropical butterflies. Although the analysis showed that these groups experienced their main diversification burst during the last 2.6 million years, coinciding with the Pleistocene glacial cycles (Garzón‐Orduña et al., 2014, Journal of Biogeography, 41, 1631–1638), a causal link between the speciation chronology and the evolutionary mechanisms proposed by the refuge hypothesis is not provided. Without more detailed studies on the environmental drivers, geographical patterns and speciation modes, establishing a causal link between speciation chronology and a particular speciation model – of which the refuge hypothesis is only one among many possibilities – is too speculative. Here I provide a six‐step conceptual framework for linking the speciation chronology with the environmental drivers and the ecological and evolutionary mechanisms potentially involved.