The aim of the present study was to detect the antibacterial activity of medicinal plants against fish microflora. A total of 4 ethanolic extracts of 6 plant species were collected from local environments of Slovakia and screened for antibacterial activity against bacterial microflora. Extracts of Melissa officinalis L., Mentha piperita L., Origanum vulgare L. and Malva mauritiana were used. Bacterial strains were isolated from common bleak (Alburnus alburnus) and common rudd (Scardinius erythrophthalmus) of Latvian origin. All bacterial strains were identified with the Matrix- Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). Among fish microflora, Acinetobacter pittii, A. baumannii, Buttiauxella agrestis, Delftia acidovorans, Enterobacter cloacae, Serratia liquefaciens, Pseudomonas alcaligenes, Ps. oryzihabitans, Staphylococcus epidermidis, St. caprae, Pantoea agglomerans, Lelliottia amnigena, Providencia rettgeri, Escherichia coli and Rahnella aquatilis were identified. It has been shown that all plant extracts exhibit different degrees of antimicrobial activity against the tested bacteria. All bacterial strains in the present study were moderate sensitive to all extracts applied. The strongest antimicrobial effect of Malva mauritiana and Melissa officinalis L. against Pseudomonas oryzihabitans (6.67±1.53 resp. 9.67±0.58 mm) were found. The best antimicrobial activity of Mentha piperita L. was against Staphylococcus epidermis (7.33±0.58 mm) and strongest antimicrobial effect of Origanum vulgare L. was same against two bacterial strains Enterobacter cloacae and Serratia liquefaciens (9.67±0.58 mm).