About 70% mortality occurred in cultured coho salmon Oncorhynchus kisutch at a marine farm in the South Sea of Korea in 2014. Diseased fish showed greyish or pale patches on the gills, with no internal signs of disease. No bacteria or viruses were isolated from diseased fish, but numerous amoebae were found on the gills. Histopathological examinations revealed extensive hyperplastic epithelium and lamellar fusion in the gills. Numerous amoebae were seen between gill filaments. The amoebae had a 630 bp partial 18S rRNA gene fragment specific to Neoparamoeba perurans. Phylogenetic analysis based on partial 18S rRNA gene nucleotide sequences revealed that this Korean amoeba belonged to the N. perurans group. This is the first report of N. perurans infection in Korea.