A comparative genomics approach was used to determine whether established extracellular vesicle biogenesis pathways are conserved in helminths. This revealed conservation of membrane and cytoskeletal organising proteins as well as the endosomal sorting complex required for transport previously described in mammalian cells. Domain level analysis of this complex in helminths, however, indicated that some species may rely on atypical proteins to support subunit interactions and cargo recruitment. Interestingly, helminths displayed phylum level divergence of proteins associated with loading RNA into extracellular vesicles. These findings provide a framework for functional studies of helminth extracellular vesicle biogenesis and cargo sorting.