The heartwood (HW) of Japanese cedar (Cryptomeria japonica) has usually a reddish color. But some trees have black-colored heartwood (BHW). BHW of Japanese cedar has a low commercial value because of the appearance. Therefore, in this study, a comparative analysis was conducted to evaluate the differences in the physical, mechanical, and inorganic element properties, and decay resistance of red-colored heartwood tree (RHW) and BHW. The physical properties showed significant difference between sapwood (SW) and HW, but there was no significant difference between RHW and BHW. From the results of mechanical properties, no significant difference was recognized in SW of RHW, HW of RHW, SW of BHW, and HW of BHW. There were decay resistance differences between RHW and BHW in HW, and between HW and SW in both RHW and BHW, respectively. The magnesium (Mg), potassium (K), and calcium (Ca) contents had significant differences between SW and HW in both RHW and BHW. In this present study, the decay resistances and the contents of Mg and K were higher in HW than in SW both for RHW and BHW, while these measurements were lower in RHW than in BHW. Therefore, BHW was considered to be worthy as a high-quality material as RHW.