When the Saints arrived in
Commerce, Illinois, in 1839, Marks was appointed as
president of the church's Commerce
Stake. (He later was president of the
Nauvoo Stake). He served in that position until 1844. He was also elected as a Nauvoo municipal alderman and as one of the regents of the
University of the City of Nauvoo in February 1841, and was a founder of the Nauvoo Agricultural and Manufacturing Association. He was appointed by revelation (D&C 124) to contribute to and be on the
Nauvoo House committee, and served as landlord of the
Mansion House. As stake president, he assisted in the laying of the cornerstones of the
Nauvoo Temple in April 1841. He was initiated into
Masonry in April 1842 and received his
endowment on May 4, 1842, as a member of the
Council of Fifty. Although a close friend of Joseph Smith, Marks occasionally found himself at odds with the prophet. Smith presented evidence of why
Sidney Rigdon should be rejected as first counselor in the
First Presidency of the church during the October 1843 General Conference. He accused Rigdon, a long-time friend of Marks, as having lost his "integrity and steadfastness" and stated that he had no confidence in Rigdon's abilities as a leader in the church or as his counselor. Regardless of these accusations, Marks motioned that Rigdon remain in his station as a counselor in the First Presidency. Rigdon was sustained to the position by the membership of the church. After the vote, Smith stood and stated, "I have thrown him off my shoulders and you have again put him on me, you may carry him, but I will not." Because Rigdon was rejected by Smith, most of the core leadership of the church, including members of the Council of Fifty and
Anointed Quorum, questioned Rigdon's standing and authority and, later, his claim to succeed Smith as head of the church. Rigdon and Marks were also known opponents of
plural marriage. Those who supported this controversial practice instituted by Smith saw such dissent as disloyal. Smith also spoke at the funeral of Marks's son. Among his remarks he said: :"I never felt more solemn. It calls to mind the death of my oldest brother [Alvin], who died in New York, and my youngest brother, Don Carlos Smith|[Don] Carloss Smith who died in Nauvoo…. It will be but a short time before we shall all in like manner be called. It may be the case with me as well as you. Some have supposed that Br[other] Joseph could not die, but this is a mistake. It is true there ha[ve] been times when I have had the promise of my life to accomplish such-and-such things, but, having accomplish[ed] those things, I have not at present any lease [on] my life. I am as liable to die as other men." This funerary sermon is considered one of the most introspective and emotionally depressed discourses by Smith, and pointed to by Mormons as foreknowledge and a
prophecy of his own death which occurred not long thereafter. In the weeks before Joseph Smith's death, Marks claimed that Joseph came to him and told him that plural marriage had proved a curse rather than a blessing to the church. Smith wanted to take decisive steps to end the practice, but, according to Marks, time ran out. Other purported pieces of evidence, such as Joseph's burning of the polygamy revelation and destroying his temple garments, seem to support Marks's story. Not all members of the church hierarchy believed Marks's testimony, though Quinn believes that
Brigham Young gave credence to it, as he later said that if Joseph "had followed the Spirit of revelation in him he never would have gone to Carthage". Ironically,
Joseph Smith III later would not believe Marks, either, since Marks implicated Joseph Smith III's father in polygamy. ==Issues with apostolic succession==