Recent studies have revealed that oligodeoxynucleotides (ODNs) designed from genome sequences have the potential to regulate cell fate. Currently, ODNs that conduct cell differentiation are nanomolecular drug candidates for regenerative medicine. Herein, we demonstrate that iSN40, an 18-base ODN derived from the Lacticaseibacillus rhamnosus GG genome, promoted the differentiation and calcification of osteoblasts that play a central role during bone formation. In the murine osteoblast cell line MC3T3-E1, iSN40 enhanced alkaline phosphatase activity at the early stage of differentiation and facilitated calcium deposition at the late stage by inducing the expression of osteogenic genes such as Msx2, osterix, collagen type 1α, osteopontin, and osteocalcin. Intriguingly, the CpG motif within iSN40 was not required for its osteogenetic activity, indicating that iSN40 functions in a TLR9-independent manner. These data suggest that iSN40, serving as an osteogenetic ODN (osteoDN), as a drug seed that target osteoblasts for bone regeneration.