Antibiotics have been at the forefront of modern medicine in providing treatment against a wide range of morbidity and mortality causing pathogens. However, the emergence of a number of antibiotic-resistant and multi-drug resistant pathogens necessitates the development of novel antibiotics. There is now a growing interest in using peptides as the next generation antibiotics. Using modern peptide chemistry techniques hundreds/thousands of antibacterial peptide variants can be rapidly produced, however, traditional methods of determining their efficacy relies on growing the pathogen and determining the minimal inhibitory concentration (MIC), which is not conducive to high throughput screening. Here we evaluate the ability of microbial flow cytometry using a Beckman Coulter Cell Lab Quanta SC MPL to detect and quantify the antibacterial activity of ten well characterised antibacterial peptides and six antimicrobial peptide analogues against a range of oral bacteria and bacteria from the ESKAPE pathogen family and motile bacteria. The microbial flow assay was shown to determine the minimum disrupting concentration (MDC) within two hours, which was significantly faster than the methods for determining minimum inhibitory concentration (MIC) or minimum bactericidal concentration (MBC), which take 22-24 hours to determine. There was no significant difference found between MDC, MIC and MBC values for all of the peptides and bacteria tested. Using flow cytometry we have been able to rapidly screen and identify antimicriobial peptides effective against a wide range of bacterial pathogens.