A detailed investigation of the morphological evolution of the coccolithophorids Calcidiscus leptoporus and C. macintyrei from the Early Miocene to the Quaternary shows that microevolutionary patterns were very complex. Speciation patterns such as cladogenesis and phyletic divergence were observed, but stasis also existed over prolonged time-intervals. Similar coccoliths developed repeatedly at stratigraphically distant intervals, leading to taxonomic uncertainies. On the basis of bivariate frequency diagrams of coccolith diameters and number of elements in the distal shields nine morphotypes S, I, L, F, A, B, C, D and E are distinguished. A tentative phylogeny was constructed for these morphotypes suggesting, that they belong to one extant species and several extinct species. The extant species is Calcidiscus leptoporus, which comprises the living morphotypes S, I, L, and F and one extinct morphotype E. Morphotype S is the most conservative one, which originated from an unknown ancestor during the Early Miocene or earlier, while morphotype I originated from S during the Early Miocene. Morphotypes L and E separated from I during the Late Miocene. An extinct lineage is proposed, including morphotypes C, D, A, and B, which all produced large coccoliths except morphotype B, which is small. Morphotypes C, D, and A are very similar to a coccolith that specialists call Calcidiscus macintyrei, but in the present phylogenetic model they may belong to separate species with similar morphology. Morphotype C developed from morphotype I during the Early Miocene and is the precursor of an extra large morphotype D, and two other morphotypes, A and B. All three forms separated from morphotype C by pronounced cladogenetic events during the Late Miocene and Pliocene, and hence may represent separate species. Morphotypes A and B are supposed to belong to an extinct morphocline and may thus be ecophenotypes of one species. Alternatively, due to the lack of paleoenvironmental and biogeographic observations in the past, it cannot be discounted that all morphotypes found in this investigation simply represent ecovariants of one species. With the present status of knowledge, it is not possible to propose a sound differential diagnosis in the plexus C. leptoporus-C. macintyrei, which would allow differentiation among species at each point in space and time. It is hoped that this study stimulates further morphometric and phylogenetical studies that will generate a more profound understanding of species in paleontology and biology in general.