The demand for novel antimicrobial compounds is rapidly growing due to the rising appearance of antibiotic resistance in bacteria; accordingly, alternative approaches are urgently needed. Antimicrobial peptides (AMPs) are promising since they are a naturally occurring part of the innate immune system and display remarkable broad-spectrum activity and high selectivity against various microbes. Marine invertebrates are a primary resource of natural AMPs. Consequently, cDNA expression (EST) libraries from the Cnidarian moon jellyfishAurelia auritaand the Ctenophore comb jellyMnemiopsis leidyiwere constructed inEscherichia coli. Cell-free size-fractionated cell extracts (< 3 kDa) of the two libraries (each with 29,952 clones) were consecutively screened for peptides preventing the biofilm formation of opportunistic pathogens using the crystal violet assay. The 3 kDa fraction of ten individual clones demonstrated promising biofilm-preventing activities againstKlebsiella oxytocaandStaphylococcus epidermidis. Sequencing the respective activity-conferring inserts allowed the identification of small ORFs encoding peptides (10 – 22 aa), which were subsequently chemically synthesized to validate their inhibitory potential. Biofilm-preventing effects againstK. oxytoca, Pseudomonas aeruginosa, S. epidermidis, andS. aureuswere verified for five synthetic peptides in a concentration-dependent manner, with peptide BiP_Aa_5 showing the strongest effects. The impact of BiP_Aa_2, BiP_Aa_5, and BiP_Aa_6 on dynamic biofilm formation ofK. oxytocawas further validated in microfluidic flow cells, demonstrating a significant reduction in biofilm thickness and volume by BiP_Aa_2 and BiP_Aa_5. Overall, the structural characteristics of the marine invertebrate-derived AMPs, their physicochemical properties, and promising anti-biofilm effects highlight them as attractive candidates for discovering new antimicrobials.