Their structures and absolute configurations were determined mainly by NMR, X-ray diffraction, and computational methods. Rubipodanones C and D, the glycosides of Rubipodanone A and a pair of C-3 epimer, are the first identified dimeric napthohydroquinone glycosides from the Rubia plants. All naphthohydroquinone dimers were evaluated for their cytotoxicities against ten tumor cell lines and effects on the tumor-associated NF-κB signaling pathway, and rubioncolin C showed the best cytotoxicity with IC50 value of 1.53 μM and NF-κB inhibitory activity with IC50 value of 2.97 μM.