Allozyme variation in 11 natural populations of hinoki, Chamaecyparis obtusa (SIEB. et ZUCC.) ENDL. was studied using 10 Ioci, and compared with that in 12 groups of hinoki plus-trees selected from artificial stands in the national project for plus-tree selection breeding. In the natural populations, it was evident that most of the genetic variation was retained within populations, and population differentiation was low, as observed in many other gymnosperms. However, there were genetic clines in allele frequencies at 4 Ioci, G6p, Pod, Got-1 and Pgm along the geographic locations of the populations. The populations were mostly separated according to the locations using two clustering methods based on genetic distances among populations. Comparison of allozyme variation between the natural populations and plus-tree groups revealed that generally the variation in the natural populations was preserved even in the plus-tree groups. However, genetic differences were observed between the natural populations and the plus-tree groups in the presence or absence of rare alleles, the mean frequencies of alleles, and the distribution of allele frequencies across the natural populations or the plus-tree groups.