Molecular phylogenetic relationships among sexually isolated subpopulations (syngens) of the morphologically defined volvocacean flagellate Pandorina morum (O. F. Müller) Bory are inferred from sequences of the internal transcribed spacer regions (ITS-1 and ITS-2) of the nuclear ribosomal DNA repeats. The resolved phylogenetic lines are composed of strains with very similar sets of traditional characters, such as zygote aggregation pattern, chromosome number and cell division timing, and are correlated with the distribution pattern of the xanthophyll loroxanthin [(3R,3′R,6′R)-β,ε-carotene-3,19,3′-triol]. Thus, loroxanthin, a phylogenetic character within the Volvocales, is also of value at the infraspecific level in P. morum, a morphologically uniform species complex, within the Volvocales.