Flathead catfish (Pylodictis olivaris) are an invasive fish species that has been introduced into the Susquehanna River Basin, Pennsylvania . Because flathead catfish are known to grow very large in size and consume many aquatic species, they have the potential to cause negative ecological impacts on aquatic communities. There are many fish species in the Susquehanna River Basin that could be susceptible to predation including species that are threatened and endangered. For this study we investigated the use of molecular techniques to identify the potential prey items consumed by flathead catfish. To do so, previously developed molecular methods were tested on several fish tissue samples of known identity . These methods were then tested on a flathead catfish diet sample. The DNA samples were sequenced, interpreted and compared against online databases to determine the identification of the species. Of the thirteen fish tissue samples tested for molecular identification, twelve resulted in useable DNA sequences. The flathead catfish diet sample was heavily degraded, but we managed to extract tissue and use molecular methods to identify a cutlips minnow. The diet sample included additional more severely degraded pieces of tissue and crayfish which required additional analyses not completed in this study. Overall, the molecular methods used for the species identification worked well and can be used to further study the dietary samples of flathead catfish.