The author reviewed the molecular phylogeny of primitive echinoids, Cidaridae of the order Cidaroida and Diadematidae of the order Diadematida. The phylogenetic relationships among four representative members of each family were examined by allozyme analysis. The genetic distances between species were calculated from allele frequencies data in enzyme genetic loci (18 loci in Cidaridae and 27 loci in Diadematidae) and molecular phylogenetic trees were constructed based on genetic distances by UPGMA clustering method. They indicated the followings: In Cidaridae, (1) Stereocidaris japonica and Prionocidaris baculosa are most closely related to each other among four species and diverged later. (2) Eucidaris metularia is more closely related to the cluster of S. japonica and Pr. baculosa than Phyllacanthus dubius.  (3) Phyllacanthus dubius is the most distant species among four species and diverged earlier time. (4) The large genetic distances observed between four members of Cidaridae demonstrated that all of them diverged at considerably old times and have old evolutionary origin. In Diadematidae, (1) Diadema setosum and D. savignyi are closely related to each other. (2) Echinothrix calamaris and E. diadema are closely related to each other. (3) Three local populations of D. setosum and two local populations of E. calamaris have not been differentiated genetically. The molecular results were compared with non-molecular evidence of morphology and paleontology.