In this review we show as ciliates can be valuable eukaryotic microorganisms for use as whole-cell biosensors or as a potential cellular source of molecular biosensors to detect pollutans ( such as heavy metals) in environmental samples. We report the different advantages of using ciliates in biomonitoring of heavy metals, in comparison with other microorganisms. We show several examples of the suitability of ciliates as potential whole-cell biosensors (analysis of heavy metal bioaccumulation using fluorophores or metallothionein gene expression revealed by reporter genes) or as a source of molecular biosensors (ciliate metallothioneins) to detect bioavailable heavy metals in environmental samples.