Microbial species diversity, both global and local, is still poorly understood. In this study all species of ciliated protozoa were recorded microscopically from ∼ 1 cm2 sediment collected from a small lake and from a marine shallow-water bay. Additional adjacent sediment samples (together representing < 50 cm2) were then incubated under a variety of culture conditions to reveal "cryptic species" that are present as resting cysts or are too rare to be found microscopically. About 85 and 57% of the total number of observed species from the limnic and marine sediment, respectively, were such cryptic species. In both cases the number of species found in < 50 cm2 of sediment represented about 75% of all ciliate species ever recorded from these two previously well-studied habitats, and about 8% of all named free-living ciliates. These observations support the assumption that in the case of microorganisms "everything is everywhere" and that their global species diversity is relatively limited.