Newly emerging bacterial diseases in aquaculture due to bacteria like Flavobacterium and Edwardsiella sp. in marine and freshwater fish and shellfish are becoming topic of interest due to their pathogenicity potential. This study describes the isolation and characterization of Flavobacterium species and Edwardsiella tarda from infected fish and environmental samples (water and soil samples). Samples were collected from different places of Tamilnadu and Nellore, Bhimavaram, East Godavari districts of Andhra Pradesh. Samples were screened for the isolation of the bacteria Flavobacterium species and Edwardsiella tarda on tryptone soya agar (TSA) and selective media. Typical yellow coloured colonies of Flavobacterium and black coloured colonies for E.tarda were isolated for further biochemical and molecular characterization. Edwardsiella tarda has been isolated from one of the soil samples and has been further confirmed by biochemical and molecular characterization by PCR. Presumptive Flavobacterium strains were further characterised by 16s rRNA amplification and sequence analysis. Experimental infection studies are undertaken for their pathogenesis and infectivity potential assessment in carps.