New approaches for treatment of infectious diseases in aquatic animals have important roles in aquaculture technology progress. In the present study, In vitro effects of different extracts of propolis, royal jelly and pollen obtained from beehives have been investigated on aquatic pathogenic bacterial isolates. The isolated bacteria identified on the basis of their biochemical properties and sequence alignment of the amplified genome fragments. Antimicrobial activities of ethanol extracts of royal jelly, propolis and pollen, and acetone extract of propolis were determined through well diffusion and microdilution methods. The isolated bacteria identified as Aeromonas and Vibrio spp., based on biochemical characterization. Alignments of the amplified sequences showed most similarites to Vibriocholeraeand Aeromonashydrophila. The results obtained from antibacterial effects of extracts showed that the acetone extract of propolis as well as the ethanol extract of royal jelly, had the greatest effect on Aeromonashydrophila (MIC=25 mg ml-1); and the ethanol extracts of pollen and royal jelly as well as the acetone extract of propolis, showed the greatest effect on Vibriocholerae (MIC=50 mg ml-1). The results of present in vitro study propose the beehive compounds (royal jelly, propolis and pollen) as powerful natural products to control pathogenic bacteria in aquaculture systems.