The caligid genus Pupulina van Beneden, 1892 currently has three accepted species. Two new species, Pupulina cliffi n. sp. and P. merira n. sp., are described from Mobula kuhlii (Müller & Henle) and M. eregoodootenkee (Bleeker) (Mobulidae) caught along the east coast of South Africa. Pupulina cliffi can be distinguished from all the other species by the absence of posterolateral processes on the genital complex, whereas P. merira has very short, rounded posterolateral processes on the genital complex compared to the three previously known species. Additionally, P. merira is the only species with the abdomen only about two-thirds the length of the genital complex and the caudal rami about the same length as the abdomen. A dichotomous key to distinguish the five species of Pupulina is provided.