This review summarizes recent progress in the debate on distribution of micro-organisms, especially protists. I present three fundamental evidences for restricted distribution of protists, viz., a study on global soil ciliate diversity which shows a “meaningful” distinction of Laurasian and Gondwanan ciliate communities; flagship and vicarious testate amoebae and ciliates which are too conspicuous to be overlooked in Europe, if they were there; and spore-forming cryptogams which show that minute sizes and high abundances do not habitually cause cosmopolitan distribution. Regional and local protist endemism and factors restricting the distribution of micro-organisms are discussed. The most misleading generalizations are a tendency to consider protists as a homogenous group with similar properties and high abundances. Actually, however, protists are highly diverse and most species have low or very low abundances, as obvious from frequency distributions which are highly similar to those of flowering plants and animals. The data available are consistent with the “moderate endemicity model” which suggests about 30% of morphological and/or genetical and/or ecological protist endemics.