The family Temnopleuridae of the order Echinoida from Japanese waters is represented by the four echinoid species belonging to the two different genera: Temnopleurus toreumaticus, T. hardwickii, T. reevesii, and Mespilia globulus. Their phylogenetic relationships were investigated by electrophoretic analyses of 16 different enzymes. From the allozyme variation in 30 genetic loci, the Nei's genetic distances between species were caluculated and the molecular phylogenetic tree for the four species was constructed. The phylogenetic tree indicated the following: (1) Among four species of the family, T. toreumaticus and T. reevesii are the most closely related to each other and diverged later. (2) T. hardwickii is more genetically differentiated from the other two congeners. (3) M. globulus is the most distant species of the four members. These allozyme results were discussed through the comparison with other non-molecular evidence, and the divergence process of the four echinoid species was speculated.