The Rainbow trout (Oncorhynchus mykiss) and the Brown trout (Salmo trutta) are the most frequently farmed among fish of the Salmonidae family in Ukraine. The main cause of cultured Salmonidae fry mortality is gill disease of various etiologies. Chlamydiae species associated with epitheliocystis in the fish of Salmonidae family are Candidatus Clavochlamydia salmonicola and Candidatus Piscichlamydia salmonis. This research is dedicated to the study of farmed Brown trout (Salmo trutta) from a small private enterprise in the Lviv region. 80 samples were randomly taken from 8 ponds, 10 specimens from each reservoir in May 2019. Samples were examined by PCR for the presence of Ca. Clavochlamydia salmonicola and Ca. Piscichlamydia salmonis bacteria DNA. The studies were carried out in two stages: at the first stage, Chlamydia-positive samples were identified, at the next stage it was determined to which species they belonged to. As a result, first, in Ukraine, the Ca. Clavochlamydia salmonicola and Ca. Piscichlamydia salmonis bacteria DNA were detected in samples taken from Brown trout. 12 out of 80 samples (15%) were Chlamydia-positive, among them, 11 samples (13.8%) contained DNA of Ca. Piscichlamydia salmonis, two samples (2.5%) – DNA of Ca. Clavochlamydia salmonicola, one sample (1.25%) contained DNA of both Ca. Piscichlamydia salmonis and Ca. Clavochlamydia salmonicola. The prevalence of Chlamydia-like organisms in samples of various age groups was different, most frequently (9 out of 12) they were found in fish sizing up to 7 cm. Prominent clinical signs of epitheliocystis were only observed in two individuals (2.5%) sizing 2 cm (exophthalmos, eye damage) and 14.3 cm (gills and skin damage). In case of coinfection with the presence of both Ca. Piscichlamydia salmonis and Ca. Clavichlamydia salmonicola, the most severe course of epitheliocystis was observed.