We isolated a new strain of an amoebozoan, Ptolemeba bulliensis Watson et al., 2014 (Tubulinea) from the gills of farmed rainbow trout (Oncorhynchus mykiss Walbaum, 1792) showing signs of nodular gill disease. The studied strain can be identified using morphological and molecular (small subunit ribosomal RNA gene sequence data) characters. We obtained for the first time actin and cytochrome c oxidase (Cox1) gene sequences for this morphospecies. An interesting feature of the Cox1 gene is the presence of group I intron that contains a 177 amino acids long open reading frame encoding a homing endonuclease. This is the first case of a group I intron in the Cox1 gene in Amoebozoa apart from Dictyostelium. In experimental study, these amoebae demonstrate a broad range of salinity tolerance. They are capable of survival and reproduction in a range of salinities between freshwater Prescott and James medium and 18‰, but could not survive or reproduce in 25‰ and above. This indicates a possibility of this species’ distribution through brackish water biotopes, and shows that in case of pathogenicity for the farmed fish, the methods of treatment based on increasing salinity may be inefficient.