Intentional communities with gender separatism

• Elizabeth Bear, Carnival (planetary colony: female-planned society with some gender separatism; matriarchy)
• David Brin, Glory Season (planetary colony: female-planned society with gender separatism)
• Lois McMaster Bujold, Ethan of Athos (planetary colony: male-planned society with only men)
• A. Bertram Chandler, Spartan Planet (aka False Fatherland) and sequel, The Last Amazon (planetary colony: a male-only society in the first story; amazon separatists try to take it over in the second)
• Rokeya Sakhawat Hossain, "Sultana's Dream" (1905) (women got men to go into purdah, and now women run Ladyland)
• Joan Slonczewski, A Door Into Ocean (planetary colony: female-planned society with only-female species)

separatist societies within larger societies

• Amazons generally are intentionally separatist
• Marion Zimmer Bradley, Free Amazons of Darkover
• Sally Miller Gearhart, The Wanderground
• Diana Rivers, Hadra
• Jean Stewart, Isis series
• Sheri S. Tepper, The Gate to Women's Country (post-apocalyptic Earth: female-run society with gender separatism)
• John Varley's Gaean trilogy volumes 2 & 3 (Wizard and Demon) have a lesbian separatist society