Crinoid taxonomy has been plagued with morphological variability as a result of intraspecific phenotypic plasticity. In an effort to test the validity of these overlapping morphological characters, we compared new mtDNA phylogenies and morphological matrices of two separate comatulid species complexes to the current alpha taxonomy. In the genus Comaster Agassiz, 1836 we examined partial mitochondrial (mtDNA) gene sequences (COI and ND2) of Comaster audax (Rowe et al., 1986), Comaster nobilis (Carpenter, 1884), and Comaster schlegelii (Carpenter, 1881), while in the genus Phanogenia Loven, 1866 we examined the two morphotypes of Phanogenia gracilis (Hartlaub, 1893). The morphological data analysis of overlapping characters revealed no trends in both species complexes, thus conflicting with current morphological species designation. Although, Comaster audax can be distinguished by its tuberculate brachitaxes and arm bases, spinous swollen axillaries and proximal brachial ossicles. The mtDNA phylogenies also conflict with current morphological species designation. Comaster nobilis and Comaster schlegelii are conspecific, while Comaster audax is paraphyletic with respect to the C. nobilis/schlegelii clade, which may explain the partitioning of some limited morphological variation to particular ocean basins. The P. gracilis morphotypes are conspecific with no geographic partitioning. However, population genetic analyses reveal genetic breaks between the Pacific Ocean and the Indian Ocean in the C. nobilis/schlegelii clade, which may explain the partitioning of morphotypes to particular ocean basins. The conflicting morphological and molecular data sets confirm that the morphological characters need to be reevaluated.