New populations of the two species of calanoid copepods known to inhabit freshwater lakes in East Antarctica, Boeckella poppei (Mrázek, 1901) and Gladioferens antarcticus Bayly, 1994, have recently been discovered. The morphology of the populations of B. poppei showed significant differences, notably a reduction in the armature of the male fifth leg, when compared with typical specimens from the Antarctic Peninsula and South America. Gladioferens antarcticus had previously been recorded from a single lake in the Bunger Hills, but has now been recorded from three further lakes in this region. A recent review of Antarctic terrestrial and limnetic zooplankton suggested that neither of these species can be considered an East Antarctic endemic, with B. poppei being listed as a recent anthropogenic introduction and G. antarcticus a ‘marine interloper’. We conclude differently: B. poppei has been present in isolated populations in East Antarctica for significant lengths of time, possibly predating the current interglacial, while G. antarcticus is a true Antarctic endemic species whose ancestors have been present in the region since before Australia separated from Antarctica.