The 68-year-old rocker filed papers in the couple’s hometown of San Mateo in California on 29 July, Rolling Stone magazine reports.
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Neil Young and Pegi Young are set to divorce after 36 years of marriage
Neil and Pegi are the parents of two grown children, daughter Amber and son Ben, while Neil is also a father to son Zeke from a previous relationship.
They first met while Pegi was working as a waitress at a diner near his California Ranch, and were married in August 1977. Pegi, 61, was not only a frequent musical collaborator with her husband, but was the inspiration behind many of his love songs, including Unknown Legend and Once An Angel.
She started touring with him in the 1990s as a backup singer, and performed with him at the Oscars in 1994, when his song Philadelphia was up for best original song. Pegi put out her first solo album in 2007 and has since released two more.
Pegi Young and Neil Young performing at the annual Bridge School Benefit Concert in 2011
Inspired by their experiences with son Ben, who has cerebral palsy, the couple co-founded the Bridge School in 1986, which helps educate children with severe speech and physical disabilities.
Neil has just completed his Crazy Horse tour in Europe and is preparing to play in the US in October. He and Pegi were scheduled to play together at the Farm Aid benefit in North Carolina on 13 September, but she was recently removed from the line-up.