To introduce the special issue this paper reviews the use of protists as bioindicators. Seven key advantages of protist bioindicators are highlighted, namely: environmental sensitivity, functional importance, distribution, size and numbers, response times, ease of analysis and preservation potential. Protist bioindicators have been used in a wide range of contexts from ecosystem restoration to fire history, and particularly environmental pollution. Most major protist groups have been used as bioindicators with diatoms, foraminifera and testate amoebae particularly widely studied. To increase uptake of protist bioindication techniques in routine environmental monitoring technique development should consider the needs of stakeholders from an early stage. Papers in this special issue reflect the diversity of both protist life and possible bioindicator applications.