Histomonas meleagridis is a protozoan parasite that causes mortality and morbidity in a wide range of gallinaceous fowl. It most notably affects turkeys, causing 80–100 % mortality in a flock. There is no commercial treatment for this parasite at the moment and attempts at a vaccine have failed. In this study we investigated the potential efficacy of novel rumen and chicken gastrointestinal tract microbiome-derived antimicrobial peptides (AMPs) against H.meleagridis. H. meleagridis was cultivated in growth flasks in Dwyer media. The concentration of the parasite was determined using a Haemocytometer, the cells were counted under the microscope. The AMP challenges were carried out in 96-well plates. The starting concentration of the AMPs were 1024 µg ml−1 down to 2 µg ml−1. The cell densities of H. meleagridis were checked at 24 h. The protozoal cell densities were checked by extracting DNA and performing qPCRs targeted against FeHyD and Rpb1 genes. Fluorescent microscopy was also used to check parasite densities as described above. Five Chicken and three Rumen AMPs resulted in decreases in protozoal cell densities following microscopy, suggesting that the peptides show potential therapeutic application for blackhead disease. Nonetheless, the qPCR primers were non-specific and resulted in bacterial DNA amplification. Consequently, in order to understand the biological function of H. meleagridis and design new qPCR primers allowing quantification, we isolated the macronuclei of a H. meleagridis strain followed by sequencing using the illumine Hi-Seq 2500 and paired ends. Future work will focus on confirming how well the AMPs work agent H. meleagridis by employing electron microscopy to observe how the AMP affect the cells.