Paramecium tetraurelia has an excitable membrane with electrical properties resembling those of nerve and muscle cells from metazoans. However, the relationship between the molecules underlying electrical excitability in Paramecium and those found in metazoans has been unexplored. Using a PCR-based screen, we identified a multigene family of putative potassium channels in the ciliate protist Paramecium tetraurelia. Two distinct genomic clones were isolated, each encoding an apparently complete channel, Pak1 and Pak2. Fragments of three additional genes were also isolated. The deduced amino acid sequences appear to define a family of novel K+ channel genes which are only distantly related to metazoan potassium channels; the K+-selective pore region is exceptionally well conserved, but outside this region, PaK1 and PaK2 bear little resemblance to the metazoan voltage-gated K+ channels, Shaker Shal, Shab or Shaw. The uniqueness of this large set of K+ channel genes may be accounted for by the distinct evolutionary pressures at play in the single celled Paramecium versus the multicellular Metazoans. Since a large number of K+ channel mutants exist in Paramecium, the sequences of the K+ channel gene family reported here may represent a significant step towards the molecular characterization of these important behavioral mutants.