A previous study showed that flaxseed (FS) combined with low-dose (LD) estrogen therapy, resembling LD transdermal estrogen therapy in postmenopaual women, inhibited loss of bone mineral density (BMD), bone mineral content (BMC), and strength in lumbar vertebrae in ovariectomized rats. Whether FS combined with an even lower dose of estrogen is effective at preserving bone or whether FS interferes with the effect of this lower dose of estrogen is unknown. Thus, this study determined whether an ultra-low-dose (ULD) estrogen therapy, half the dose previously studied, in combination with FS preserved bone mass and strength in the lumbar vertebrae in ovariectomized rats. Rats were treated for 12 wk with (1) basal diet (BD) (ovariectomized control), (2) BD + ULD estrogen implant, or (3) BD containing 10% FS + ULD estrogen implant. A sham-operated control group was fed BD. Unlike ULD, FS + ULD attenuated loss of BMD and strength at the lumbar vertebrae and BMD in femurs and tibias. FS + ULD resulted in higher percentages of n-3 fatty acids including alpha-linolenic acid and eicosapentaenoic acid and lower percentages of n-6 fatty acids including linoleic acid compared to all other groups. Differences in fatty acid composition at the lumbar vertebrae and tibia were significantly related to BMD, BMC, and strength. No treatment-induced effects on uterus weight were observed, but histological analyses are needed to confirm safety. In conclusion, FS did not antagonize the activity of ULD, and their combination attenuated the loss of BMD and strength at the lumbar vertebrae, which was associated with differences in bone fatty acid composition.