The diversity of parasites found on Nyctiphanes simplex and Nematoscelis difficilis (Order Euphausiacea) was compared during 10 oceanographic cruises made off both coasts of the Baja California peninsula, Mexico. We tested the hypothesis that N. simplex has a more diverse parasitic assemblage than N. difficilis because it is a neritic species, has larger population abundance, and tends to form denser and more compact swarms than N. difficilis. These biological and behavioral features may enhance parasite transmission within swarms. We detected 6 types of ectoparasites: (1) epibiotic diatoms Licmophora sp.; (2) Ephelotidae suctorian ciliates; (3) Foettingeriidae exuviotrophic apostome ciliates; (4) an unidentified epicaridean cryptoniscus larvae (isopoda); and 2 castrators: (5) the ectoparasitic Dajidae isopod Notophryxus lateralis and (6) the ellobiopsid mesoparasite Thalassomyces fagei. We also detected 7 types of endoparasites: (1) an undescribed Collinia ciliate (Apostomatida); 3 types of Cestoda: (2) a Tetrarhynchobothruium sp. (Trypanorhyncha), (3) Echinobothrium sp. (Diphyllidea: Echinobothyriidae), and (4) unidentified metacestode; (5) a Trematoda Paronatrema-like metacercaria (Syncoeliidae); (6) the nematode Anisakis simplex (L3); and (7) Polymorphidae acantocephalan larvae (acanthor, acanthella, and cystacanth larval stages). N. simplex is affected by all types of parasites, except the isopod N. lateralis, having a considerably larger parasitic diversity and prevalence rates than N. difficilis, which is only infested with 3 types of ectoparasites and T. fagei. Euphausiid swarming is an adaptive behavior for reproduction, protection against predators, and increased efficiency in food searching, but has a negative effect due to parasitism. Although the advantages of aggregation must overcome the reduction of population and individual fitness induced by parasites, we demonstrated that all types of parasites can affect approximately 14% of N. simplex individuals. Collinia spp. endoparasitoids must occasionally have a significant influence on population mortality with potential epizootic events.