Brannan was married to Eliza Crane, daughter of Colonel
Ichabod B. Crane (colonel of the 1st U.S. Artillery), on September 16, 1850. They had one daughter named Alida. While Brannan was posted in Key West, Florida, from 1856, Eliza and their daughter lived in
Staten Island, New York, with her mother. On July 20, 1858, Eliza Brannan disappeared while she was out shopping in New York City. After days of searching, it was believed by officials that she was dead. John Brannan reportedly feared she had committed suicide in a moment of temporary insanity. In 1860, however, Eliza Brannan contacted her brother (Dr. Charles Crane) and notified him that she was, in fact, alive: having originally fled to Italy, she was now remarried and living in Paris, France. Dr. Crane notified Brannan of the news that his wife still lived. Brannan soon learned that the man who Eliza had remarried was Powell T. Wyman. A career artillery officer of the 1st U.S. Artillery, Wyman met Eliza Brannan through a mutual acquaintance and the two corresponded after her flight to Europe. In 1860, First Lieutenant Wyman was denied a leave of absence to visit his lover, and instead resigned his commission and traveled to Italy to join (and later marry) Eliza Brannan. At some point between 1860 and 1862, Wyman and Eliza Brannan returned to the United States, where they lived openly as a married couple. Brannan never reconciled with his wife; he obtained a decree of divorce in 1863. In 1870, Brannan was remarried to Evelyn (Eva) Way; the couple lived in New York following Brannan's retirement. Brannan died of heart failure in New York in 1892. He was buried temporarily at
Woodlawn Cemetery, and later reinterred on the grounds of his alma mater at the
West Point Cemetery. == Legacy ==