DNA-based studies have revealed that biodiversity has been underestimated in most groups of pelagic organisms. Recently, higher diversity has also been molecularly detected in planktonic foraminifera, which challenges the morphological concepts applied to define the species level in this group, and provides new insight in interpretation of their fossil record. Here, we present a genetic analysis based on small subunit ribosomal DNA genes from 189 individuals of the morphospecies Globigerinella siphonifera, collected along an Atlantic transect covering 57° of latitude. Four different, strictly homogeneous genotypes, called types I, II, III and IV, were detected. Their origin occurred in the late Miocene according to the absolute molecular clock estimation based on genetic distances calibrated within the fossil record. Biogeographic analysis shows that each G. siphonifera genotype is adapted to a specific environment: type I prefers oligotrophic waters, type II, although cosmopolitan, is probably adapted to mesotrophic waters, types III and IV live in highly productive waters. This emphasizes the importance of the water column stability and resulting trophic structure for planktonic foraminiferal evolution. The phenomenon of adaptive radiation of slightly different morphotypes described here in G. siphonifera is compared to analogous evolutionary patterns molecularly revealed in two other planktonic foraminifera, Orbulina universa and Globorotalia truncatulinoides. It implies that closely related morphotypes within classically defined planktonic foraminiferal taxa may be different species and can be markers of highly different environments.