In this review, I report on the molecular phylogeny on the sea-urchins of the two families: Temnopleuridae and Echinometridae by allozyme analysis. The molecular phylogenetic tree of the Temnopleuridae shows that T.toreumaticus and T.reevesii are closely related to each other and T.hardwickii is genetically differentiated. The D value between Temnopleurus and Mespilia was comparable to those of different genera. The molecular phylogenetic tree of the Echinometridae shows that A.crassispina and E.mathaei are most closely related, Ec.aciculatus and Ec.molaris are the same species at the molecular level, and H.mammillatus and C.mertensii are closely related. These allozyme results were discussed through the comparison with other molecular and non-molecular data, and the divergence process of these sea-urchins from two families was also speculated.