Significance Previous studies demonstrate that endogenous wingless-type MMTV integration site family (WNT)16 is a crucial regulator of cortical bone mass. Surprisingly, we demonstrate that overexpression of WNT16 increases mainly trabecular bone mass. Both estrogen and WNT16 are crucial regulators of bone mass, but the possible interaction between WNT16-signaling and estrogen-signaling is unknown. To determine the possible interaction between WNT16 and estrogen signaling in bone, we developed and used two genetically modified mouse models with either constantly high osteoblastic Wnt16 expression or no Wnt16 expression. We demonstrated that the bone-sparing effects of estrogen and WNT16 are independent of each other. As WNT16 signaling in bone does not require normal estrogen action, we propose that WNT16-targeted therapies might be useful for treatment of postmenopausal trabecular bone loss.