Geometric morphometric analyses were conducted on cultured populations of five Micrasterias species (M. crux-melitensis, M. papillifera, M. rotata, M. thomasiana, M. truncata). The patterns in the morphological variation measured using the morphospaces spanned by a PCA of morphometric data for individual populations were compared. In addition, the 18S rDNA sequences of these species are reported. The phenetic comparisons demonstrated the overall great similarity of morphometric indicators extracted from isolated polar lobe data and 18S rDNA genetic distances, and also indicated that the morphometric data of complete semicells were less well correlated with 18S rDNA distances. The phylogenetic analysis revealed clustering of the Micrasterias sequences into two clades, which correspond to qualitative patterns in the morphological variation of isolated polar lobe data. We propose that patterns of variation in the polar lobes of Micrasterias should be used in phenotype analyses of morphologically closely similar or cryptic species.