Jilly's Rockworld and the Music Box both cite financial reasons for their closure.
Jilly's, formerly Fagin's, opened in 1970 on Manchester's Oxford Road and saw early performances by Joy Division and Depeche Mode.
The venue housed Jilly's Rockworld upstairs, a 1,300 capacity rock venue, and the Music Box downstairs.
Owner John Bagnall says attendance numbers had fallen in recent years.
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