Tail and fin rot is one of the most economically important disease throughout the world. Occurrence of tail and fin rot and emergence of antibiotic resistance in trout farming has mandated extensive survey, characterization of dominant causative agents followed by screening of effective antibiotics. In present study, predominant fin and tail rot causing bacterial pathogens were isolated from samples collected from fifteen rainbow trout farms of major trout pocket areas i.e. Rasuwa, Nuwakot, Dhadhing, Sindhupalchowk, Lalitpur and Kaski districts of Nepal. All the isolates were further tested for pathogenicity, which showed virulence in fancy carp (Cyprinus carpio haematopterus). Pseudomonas spp and vibrio spp showed more virulence. Antibiotic susceptibility test revealed that all the commonly used antibiotics (Amoxicillin, Azithromycin, Neomycin, Oxytetracycline and Streptomycin) were completely resistant. Among presently used antibiotics, Cephalexin was resistance in all the farms while Doxycycline was found completely resistant in two farms and Moxifloxacin was effective in general. Positive correlation between disease occurrence and water parameters were observed among various trout farms. Lack of knowledge regarding use of antibiotics, development of multidrug resistance bacteria and downstream effect of antibiotics used in trout farms was observed among farm's owner and farmers, implicating a need to develop an effective protocol in fresh water aquaculture in Nepal.