Bottom-dwelling teleosts, particularly flatfishes or cod living in temperate to cold seawater, sometimes develop tumor-like lesions on the body surface or in the branchial cavity. These lesions usually contain masses of so called 'X-cells' of unknown origin. We amplified a gene for small subunit ribosomal RNA (18S rRNA) from X-cell lesions of the flathead flounder Hippoglossoides dubius. Phylogenetic analysis clearly classified the obtained sequence as a protozoan, although the organism had no clear affinity with any known protistan groups. In situ hybridization showed that probes specific for the protozoan 18S rRNA hybridized only with X-cells, and not with the host-fish cells, indicating that X-cells harbor the protozoan rRNA. On the other hand, a probe specific for vertebrate 18S rRNA hybridized with the host-fish cells, but not with X-cells. This is conclusive evidence that X-cells are parasitic protozoans.