Changes in the size and in the shape of the cross of the early Danian Cruciplacolithus lineage have been studied along with bulk carbon isotope data at two reference Cretaceous–Paleogene boundary sections: Bidart, SW France (Basque Basin) and Elles, central Tunisia (SW Tethys). Our study documents a progressive increase in the size of this lineage in the early Danian and allows for the definition of a new sub-lineage with a narrow central area and a broad axial cross composed of two species: a small, primitive and rare form, Cruciplacolithus praebornemannii n.sp. and a large common form Cruciplacolithus bornemannii n.sp. Successive first occurrences in the lineage of “axial cross” Cruciplacolithus can be correlated between the two sections. This correlation shows that the recovery phase in carbon isotopes following the Cretaceous–Paleogene boundary negative excursion is delayed in the southwestern Tethys compared to the Basque Basin. The delayed recovery in carbon isotopes at the Elles section could be related to the lengthened environmental stress in shelfal settings as compared to the pelagic settings of the Basque-Cantabrian basin. The emergence of Cruciplacolithus, the occurrence of the different lineages in this genus and the change in dominance from small to large forms are likely to be all related to the progressive ecosystem recovery in the early Danian.