Ciliates are unicellular protists of the phylum Ciliophora and found in high abundances in water systems world-wide. Today their important ecological role in all aquatic systems is well known. However, morphological species identification in ciliates is difficult due to sometimes tiny morphological characteristics. We here present a simplified method visualizing all important species classification patterns. We focused on species identification in the genus Euplotes using immunocytochemistry and confocal laser scanning microscopy. With these tools, we identify and describe the shape of the interphase macronucleus, the number and distribution of the ventral cirri as well as the species-specific body surface tubulin pattern. We visualize and describe three species difficult to distinguish: Euplotes octocarinatus, Euplotes aediculatus and Euplotes daidaleos. Species identification was subsequently validated with the help of 18S rDNA genome sequencing. We anticipate that this method can also be applied for the identification of different ciliate species in a cost and time effective manner.