The presence and role of endoparasites in pelagic macrozooplankton within the Southern Ocean are poorly understood. Accounts of such parasites are generally restricted to the Antarctic krill species Euphausia superba, with little information on other possible host species. Endoparasitic gregarines were recorded for the first time in the euphausiids Euphausia triacantha and Euphausia valentini and the salp Salpa thompsoni during the Kerguelen Axis Antarctic research cruise (February–March 2016). Gregarines found in E. triacantha and E. valentini were morphologically similar to those previously identified in Antarctic krill, E. superba. Despite overlapping distributions, the smaller euphausiid Thysanoessa macrura possessed a different gregarine endoparasite, indicating parasite–host specificity in Southern Ocean euphausiids. Most notable was the discovery of large gregarines in the stomachs of aggregate individuals of S. thompsoni. The presence of gregarines in these dominant macrozooplankton indicates that endoparasitism within the Southern Ocean is more common than previously thought. Gregarines were observed in guts of krill and salps collected between 57.9 and 63.6°S. The continual presence of gregarines in the species examined indicates that these host-parasite interactions are not isolated events with differing life stages of gregarines within the same intestinal tract of some species indicating periodic infection. The impacts of gregarine parasitism on these newly identified hosts are unclear and require further investigation to understand the spatial and temporal patterns of gregarine-host interactions.