The aim of this study was to examine the existence of the Flavobacterium spp. at two different rainbow trout farm hatcheries in Caglarca village, Mersin, between December 2006 and April 2007. For this goal samples were collected from milt, ovarian fluid, and all phases from egg till 3 months old fries and from the water used in both farms. In consequence of disease outbreak at the II. farm, 30–40 days after fry started feeding, mortality occured as high as 50 %. Clinical signs at fries were observed as dark coloration of the skin, exophthalmia, erosions on dorsal and caudal fins, lethargy, swimming close to the water surface, weakness and loss of appetite. As autopsy signs anaemia and haemorrhage on gills and liver, and splenomegali were observed. Totally 347 samples, including 77 water and 270 fish samples taken from the hatcheries, were examined. Flavobacterium spp. were isolated and identified using conventional culture methods. 141 (33.71%) Flavobacterium spp. have been isolated from 117 samples. 46 Flavobacterium spp. were isolated from 39 (50.64%) water samples and 95 from 78 (28.88%) fish samples. Off the total isolates 76 (42.93%) were identified as F. aquatile, 30 (16.94%) as F. columnare, 20 (11.29%) as F. branchiophilum, 12 (6.77%) as F. johnsoniae and 3 (1.69%) as F. saccarophilum. Antimicrobial susceptibility test was carried out by agar disc diffusion method. In according to antimicrobial susceptibility test, Flavobacterium spp. strains were sensitive to gentamicin, streptomycin, neomycin, sulphamethoxazoletrimethoprim, oxytetracycline, ofloxacin, clindamycin, amoxycilin/clavulinic acid, and resistant to erythromycine, penicillin and vancomycin, respectively.