Ecological studies of peatland testate amoebae are generally based on totals of 150 individuals per sample. However, thesuitability of this standard has never been assessed for alkaline habitats such as spring fens. We explored the differences intestate amoeba diversity between Sphagnum and brown-moss microhabitats at a mire site with a highly diversified moss layerwhich reflects the small-scale heterogeneity in groundwater chemistry. Relationships between sampling efficiency and samplecompleteness were explored using individual-based species accumulation curves and the effort required to gain an extra specieswas assessed. Testate amoeba diversity differed substantially between microhabitats, with brown mosses hosting on averagetwice as many species and requiring greater shell totals to reach comparable sample analysis efficiency as for Sphagnum.Thus, for samples from alkaline conditions an increase in shell totals would be required and even an overall doubling up to300 individuals might be considered for reliable community description. Our small-scale data are likely not robust enough toprovide an ultimate solution for the optimization of shell totals. However, the results proved that testate amoebae communitiesfrom acidic and alkaline environments differ sharply in both species richness and composition and they might call for differentmethodological approaches.