Parasitic flatworms (Phylum Platyhelminthes: Subclass Digenea) are scientifically important organisms in aquatic habitats because they represent potential human (i.e. Swimmer's Itch) and wildlife pathogens. Furthermore, larval stages (cercariae) released from snail intermediate hosts represent substantial biomass, contribute to energy flow in food webs, and potentially serve as biological indicators of ecosystem health. Identification of different cercariae is has traditionally been done by morphological traits or classical genotyping. These approaches are difficult, time consuming and expensive. This presents a barrier to researchers in the field working on non-model organisms. Matrix Assisted Laser Desorption Ionization – Time of flight (MALDI-TOF) mass spectrometric based identification of microorganisms has been successfully used to identify single- and multi-cellular organisms more quickly and accurately than traditional methods. Here we describe the protein extraction and MALDI-TOF identification of cercariae from four morphologically distinct parasite taxa. We have also assembled multiple cercariae MALDI-TOF spectra into individual Main Spectral Libraries (MSP) to differentiate each unique cercariae. Finally, we describe how these MSPs can be used to quickly and accurately identify unknown cercariae and thus remove a barrier to parasitic flatworm research progress.