Calcareous nannoplankton have been one of the dominant primary producers in the surface oceans since the late Triassic. The bolide impact at the Cretaceous-Paleogene (K/Pg) boundary ~66.0 Ma, led to the elimination of > 90% of nannoplankton species: the largest extinction event in their evolutionary history.  One of the few nannoplankton genera to survive the K/Pg mass extinction and even thrive in its aftermath was Braarudosphaera, which precipitates pentagonal calcite plates (pentaliths).  The only Braarudosphaera species to span the K/Pg boundary (B. bigelowii) is extant, and has formed geographically and temporally restricted “blooms” throughout geologic time. Four morphologically and genetically distinct cryptic species of B. bigelowii have been identified in the modern ocean. However, it is uncertain whether these cryptic species have disparate eco-physiological tolerances that have allowed them to adapt to varying environmental conditions. For the first time, we assess changes in the size and shape of Braarudosphaera pentaliths following the K/Pg mass extinction at three geographically and environmentally disparate sites that have early Paleocene Braarudosphaera blooms. Our results show that different Braarudosphaera morphotypes were dominant in the Gulf of Mexico compared to the paleo-Tethys, likely due to regional environmental differences. In addition, we provide evidence that the dominant Braarudosphaera morphotypes shifted in response to changes in upper water column stratification. This ability to rapidly adapt to unstable environments likely helped Braarudosphaera thrive in the aftermath of the K/Pg extinction, and explains why this lineage has enjoyed such a long evolutionary history.