She married actor Lou Diamond Phillips in 1986. Two years later, she met Etheridge while assisting on the music video for the single "Bring Me Some Water", and split with Phillips in 1990 to start a relationship with Etheridge. Cypher directed the 1995 film Teresa's Tattoo, starring Phillips, C. Thomas Howell, and Kiefer Sutherland.
Cypher was a gay rights advocate, and became famous for being one half of one of the first publicly lesbian Celebrity couples. In 1995 she and Etheridge appeared in a "We'd Rather Go Naked Than Wear Fur" poster campaign for PETA.
During her partnership with Melissa Etheridge, Cypher gave birth to two children via artificial insemination: a daughter, Bailey Jean, born in February 1997, and a son, Beckett, born November 1998. Although initially reluctant to discuss it, the couple eventually revealed that the biological father of both children was musician David Crosby. However, Cypher later told Etheridge in a 1999 therapy session that she was "not gay", and the couple split in September 2000.
