Sleep plays an integral role in supporting well-being, and sleep difficulties are common in mothers of individuals with developmental disabilities, including fragile X syndrome (FXS). This study assessed whether the effects of sleep quality on physical health and depression are exacerbated by genetic risk factors (CGG repeats) in FMR1 premutation carrier mothers of individuals with FXS. Poor sleep quality predicted a greater number of physical health conditions for mothers with CGG repeats in the mid-premutation range (90–110 repeats), but not for those in the lower (< 90 repeats) or higher (> 110 repeats) ends of the range. A significant association between poor sleep quality and maternal depressive symptoms was also observed, but there was no evidence that this effect varied by level of genetic vulnerability. This research extends our understanding of individual differences in the effects of sleep quality among mothers of individuals with FXS.