Eight SSU rDNA genetic types have been described in the planktonic foraminifera Neogloboquadrina pachyderma, but the level of correlation between genetic diversity and morphological variation remains unknown in this morphospecies. In this study, we combine molecular and morphometric analyses of specimens of N. pachyderma sampled during two consecutive years across a latitudinal gradient in the Indian sector of the Southern Ocean. We observe that three genetic types of N. pachyderma inhabit the (sub-)polar waters of the southern Indian Ocean where they have equivalent regional distributions to those previously observed in the South Atlantic. The geographic ranges of these genetic types are largely overlapping. Our morphometric data show that contrary to other planktonic foraminiferal morphospecies, there is no relationship between genetic diversity and morphological differentiation in at least two of the austral representatives of N. pachyderma (Type III and Type IV) despite a high morphological variability and large genetic distance between these types. These genetic types of N. pachyderma in the southern Indian Ocean thus constitute true cryptic species of planktonic foraminifera.