Jomonlithus littoralis is a coccolithophore exhibiting unusual coccolith morphology that has previously only been reported from Japanese coastal waters. Jomonlithus is a mono-specific genus that has remained incertae sedis within the Prymnesiophyceae since its original description. We isolated a culture of the calcifying (diploid) stage of this species from Mediterranean coastal waters that subsequently produced a non-calcifying life cycle stage in culture. The non-calcifying (haploid) stage of J. littoralis is described for the first time through light and electron microscope observations of cytology, scale ornamentation and ultrastructure. A 28s rDNA molecular phylogeny is presented and the systematic affinities of Jomonlithus are discussed. This genus is placed in the Hymenomonadaceae and the diagnosis of this family is emended.