Different methods of estimating protozoan diversity in soil are discussed in this paper, with the major emphasis on heterotrophic flagellates. Although many species of ciliates and testate amoebae seem to be unique to the soil environment, the communities of heterotrophic flagellates and naked amoebae are probably best considered as restricted versions of their aquatic counterparts. Soil protozoa are difficult to observe directly, hence culture techniques are usually used. These techniques enable us to explore certain functional aspects, but their major drawback is that some soil protozoa cannot be cultured. Molecular methods, however, have the potential to detect such non-culturable forms.