We report the first description in Spain of Fry mortality syndrome (FMS) in rainbow trout. The most relevant clinical signs of diseased fish were abdominal distension, dark appearance, and bilateral exophthalmia with slight periocular haemorrhages. Mortalities increased when the water temperature decreased below 10°C, and the total cumulative fish losses was about 25% of the affected population. Yellow-pigmented bacteria were successfully recovered in pure culture on modified Anacker and Oral's medium from the spleen of all the fry analysed. No growth was obtained on Tryptic Soy Agar or Broth. The bacteria were identified morphologically, biochemically and enzymatically as Flexibacter psychrophilus. However, the Spanish isolates must belong to a different antigenic group that the reference type strain NCIMB 1947. The treatment with chloramphenicol, but not with flumequine, resulted to be effective to control fish mortalities.