Pleistocene microrefugia (or cryptic refugia) may be distinguished from macrorefugia (or conventional refugia) on the basis of two characteristics. First, microrefugia were smaller than macrorefugia and consequently supported smaller refugial populations. Second, microrefugia harboured less diverse biotic communities than macrorefugia. We propose that these characteristics have important implications for the ecology and evolution of species and populations that have a history of isolation in microrefugia. We propose four hypotheses regarding the evolution of microrefugial populations: (1) small effective population sizes associated with survival in microrefugia lead to reduced genetic diversity and influence the evolution of mating systems; (2) differences in environmental conditions between macro- and microrefugia lead to local adaptation; (3) reduced diversity increases ecological opportunity and promotes ecological divergence in microrefugia; and (4) reduced species diversity in microrefugia allows more specific species interactions and promotes coevolution among species. We urge biogeographers to study the evolutionary implications of isolation in microrefugia.