A. niger has biotechnological importance as it produces various enzymes, organic acids and removes waste materials. Citric acid and many A. niger enzymes are recognized as GRAS by the United States Food and Drug Administration. Aspergillus species have received much attention as sources of new antimicrobial agents (Al-Fakih and Almaqtri 2019). There are only a few studies showing that A. niger has antimicrobial properties. Subhash et al. (2022) reported that evaluated antibacterial activity of A. niger culture filtrate (ACF) against enteric pathogens (Klebsiella pneumoniae, Pseudomonas aeruginosa, Vibrio cholerae, Salmonella enterica, Shigella dysenteriae, Escherichia coli, Staphylococcus aureus, Klebsiella variicola). They have demonstrated that ACF inhibits the growth of enteric pathogens (Subhash et al. 2022). Gun Lee et al.(1999) reported that a new antifungal peptide (named Anafp) was purified from the culture supernatant of A. niger. Anafp exhibited strong growth inhibitory activities against filamentous fungi as well as yeast strains in the MIC = 4 to 15 µM range. In contrast, Anafp did not show antibacterial activity against E. coli and Bacillus subtilis even at MIC = 50 µM (Gun Lee et al. 1999). Kalyani and Hemalatha (2017) reported that antibacterial and antifungal activity of crude extract of A. niger (MTCC-961) (Kalyani and Hemalatha 2017). There are studies in the literature on the antimicrobial effect of culture filtrates obtained by A. niger. However, purification of AMP has rarely been studied. According to agar diffusion results, antimicrobial efficacy difference between flask culture and fermenter culture are occurred probably due to variable parameters such as pH and dissolved oxygen level in growth conditions. Although these parameters were controlled in the fermenter culture, the results were not more effective. Fungi and other microorganisms produce metabolites that inhibit the growth of other microorganisms for nutrient competition and habitat in the natural environment (Al-Fakih and Almaqtri 2019; Cesa-Luna et al. 2020). The amount of AMP produced may vary, as the need for nutrients and oxygen is limited in the flask culture. Yazici et al. reported that (2021), CFS of the fungus identified as A. tubingensis showed a zone larger than 20 mm against S.aureus and MRSA (Yazici et al. 2021). Kalyani and Hemalatha (2017) reported that the antimicrobial activity of A. niger (MTCC-961)'s CFS against various bacterial and fungal species was determined and the inhibition zone value for S.aureus (MTCC-3160) was found to be 12 mm (Kalyani and Hemalatha 2017). Al-Shaibani et al. (2013) determined the inhibitory effect of the CFS of A. niger, obtained from the inflamed eyes of patients against P. aeruginosa, S. aureus, S. epidermidis, and Bacillus sp., which isolated from patients of microbial keratitis. The results show that A. niger possessed inhibitory effects against P. aeruginosa, S. aureus, S. epidermidis, and Bacillus sp., with inhibition zones of 15, 25, 30, and 32 mm, respectively (Al-Shaibani et al. 2013). Omeike et al. reported that (2019) antibacterial activity of Geotrichum candidum OMON-1, Talaromyces pinophilus OKHAIN-12, and Penicillium citrinum PETER-OOA1 fungal extracts as 32 ± 0.12, 24 ± 0.2, 12 ± 0.17 mm zone of inhibition against S. aureus, respectively . The best result from our data is the zone value of 25 mm and it is similar to the values in the literature. The results of the experiment found clear support that the fungus culture filtrates differed in antimicrobial effects against various bacterial strains. In the study of Park et al. (2008), it was determined that the production of bacterial culture at different scales and physiological conditions changed the antimicrobial activity (Park et al. 1998). In the study of Liu et al. (2012), the antimicrobial activity of Laparaxin produced from Lactobacillus paracasei was investigated and it was found that this polypeptide obtained from the fermenter, where pH was fixed at 6, showed less antimicrobial activity compared to the polypeptide obtained from the non-pH control fermenter (Liu et al. 2012). Based on these studies, the reason for the differences in the results of the SDS-band profile culture grown in a flask and fermenter culture can be attributed to the different physiological conditions in which they exist. A MIC is generally considered to be the most basic laboratory measurement of the activity of an antimicrobial agent against a microorganism. Drugs with a lower MIC value are more effective antimicrobial agents, as a lower MIC value indicates that less drug dose is needed to inhibit the growth of the microorganism (Kowalska-Krochmal and Dudek-Wicher 2021). The correlation was observed between molecular weights and antimicrobial activities of AMPs. However, most researchers report an increase in antimicrobial activity with decreasing molecular weight (Sultana et al. 2021). MICs of some AMPs such as LL-37(4.4 kDa), indolicidin(1.9 kDa), pexiganan(2.2 kDa) against S. aureus ATCC 25923 are 14 µg/ml, 16 µg/ml, 32 µg/ml, respectively (Ebbensgaard et al. 2015). Mygind et al. (2005) reported that AMP purified from Pseudoplectania nigrella and characterized as plectasin (4.3 kDa) gave a MIC of 4–32 µg/mL against various MRSA strains (Mygind et al. 2005). According to Mataraci and Dosler's study (2012), indolicidin and nisin (3.3 kDa) cationic polypeptides have MICs of 16 µg/ml, 16 µg/ml against MRSA, respectively (Mataraci and Dosler 2012). Yazici et al. (2020) reported that AMP(11 kDa) purified by the species identified as A. tubingensis has 32 µg/ml and 128 µg/ml MIC values against S. aureus ATCC 25923 and MRSA, respectively (Yazici et al. 2021). These studies confirm the relation between molecular weights and antimicrobial activities. However, these findings indicate that the MIC value of purified AMP in our study is consistent with other studies. Omeike et al.(2021) reported that an AMP compound characterized as Tripeptide GP-2B produced by G. candidum OMON-1 has 8 µg/mL, 32 µg/mL, 32 µg/mL MIC values against S. aureus ATCC 25923, S. aureus ATCC 6238, various strains of MRSA, respectively (Omeike et al. 2021). In line with previous studies MICs of purified AMP gave the same values against S. aureus 25923 and MRSA.