Caves are the best known subterranean habitats, harbouring animals with a convergent morphology of reduced eyes and pigment and elongated appendages (troglomorphy). We have identified a group of aphotic aquatic habitats close to the surface [shallow subterranean habitats (SSHs)] that also harbour troglomorphic species, but with intimate surface connections, typically small in size but very abundant, with high levels of organic matter compared to caves. SSHs are hypotelminorheic, hyporheic, and epikarstic habitats. All SSHs show a pattern of environmental variation intermediate between that of surface and deep subterranean habitats, and all show seasonal and sometimes daily fluctuations in temperature but with truncated extremes. Initial colonization of these habitats was likely the result of environmental changes, especially increasing aridity, perhaps during the Pleistocene and the Messinian salinity crisis. The evolution of the troglomorphic morphology of reduced eyes and pigment and elaborated extra-sensory structures likely occurred in situ rather than by dispersal from other habitats. SSHs may be a stepping stone to colonization of deeper subterranean habitats. Copyright © 2011 John Wiley & Sons, Ltd.