Woolley was married and sealed to his first wife, Julia E. Sirls, in March 1851 and was endowed at the same time. He went on later to marry Ann Everington in 1886. In 1910, the widowed Woolley married Annie Fisher, with Joseph F. Smith performing the civil ceremony. Woolley was uncle to LDS Church President Spencer W. Kimball, and apostles J. Reuben Clark and John W. Taylor. He was also the stepfather to the B. H. Roberts, a member of the First Council of the Seventy.
Involvement with Mormon fundamentalism
Woolley is perhaps best known as the father of Mormon fundamentalism and amongst most fundamentalists is considered an apostle, prophet, and president of the priesthood. At the age of eight, Woolley received a patriarchal blessing from Joseph Smith, Sr., who at the time was the Presiding Patriarch of the Church of Jesus Christ of Latter-day Saints. Within this blessing, Woolley was promised he would "be called to responsible stations," that it would involve having to "receive keys," as well as "glory and honor" and "worlds of knowledge and power", and that he would one day "be called the Lord's anointed." Fundamentalist Mormons see this as a prophecy of the later role he would play as their leader. According to an account given by his son Lorin C. Woolley in 1929, when John Taylor was in hiding there were very few homes in which he felt his safety was secure, and very few people in whom he placed his confidence, Woolley was one of these men. His son Lorin acted as a messenger and sometimes a bodyguard for Taylor. It was in John Woolley's home that Jesus Christ and Joseph Smith allegedly visited Taylor on the night of September 26, 1886, and where the following day Taylor allegedly set apart five men as apostles, with a special commission to keep alive celestialplural marriage by granting them the authority to set apart others in perpetuity. This account is disputed by LDS Church apologists. In 1890, LDS Church President Wilford Woodruff issued what has become known as The Manifesto, officially calling for an end to the practice of plural marriage by church members in the United States. Because certain members did not take The Manifesto seriously, in 1904 another proclamation, the Second Manifesto, was put forth by church president Joseph F. Smith, which stated that those who did not cease the continuation of the practice would be excommunicated from the church. Woolley did not comply and was excommunicated from the LDS Church on March 30, 1914. When Woolley died, his son Lorin Woolley succeeded him as a leader among Mormon fundamentalists.