Date: January 02, 2017 11:23PM
I just found this out,
"Grave of Joseph Smith
Located in the Smith Family Cemetery at Nauvoo, Illinois.
Fearing the threats of grave desecration made by Joseph's enemies, Joseph's and Hyrum's family placed sandbags in the caskets buried in the city cemetery. Joseph and Hyrum's remains were secretly buried under the basement of the Nauvoo House. After Emma's death the Smith family disinterred Joseph's and Hyrum's remains and re-interred all three under a shed on the property. There were no written records marking the graves and the exact location became lost from memory. In 1928, Joseph's family feared the rising Mississippi River would destroy the graves, so they commissioned an excavation to locate the bodies of Joseph, Emma and Hyrum and had them re-interred in a permanent plot in the Smith Family Cemetery, at the site shown in the following pictures."
Emma's interred with Joseph, after all was said and done.
And Hyrum too.http://www.moroni10.com/graves/Joseph_Smith.html