The family Cidaridae of the order Cidaroida from Japanese waters includes four common echinoid species belonging to four different genera: Stereocidaris japonica, Eucidaris metularia, Prionocidaris baculosa, and Phyllacanthus dubius. Phylogenetic relationship among the four species were investigated by allozyme analysis. From the allozyme variation in 18 genetic loci, Nei's genetic distances between species were calculated. The genetic distances were higher than those observed between confamilial genera in many other echinoids, but comparable to those between different families. The result suggests that the four cidarids diverged in earlier time from one another and generally have older evolutionary origin than members of families of the orders Echinoida and Diadematoida. A molecular phylogenetic tree for the four cidarids indicated the following: (1) S. japonica and Pr. baculosa are the most closely related to each other and diverged later. (2) E. metularia is more closely related to the cluster of S. japonica and Pr. baculosa than Ph. dubius. (4) Ph. dubius is the most distant among four species and diverged first. These allozyme results are discussed through the comparison with other non-molecular evidence.