Hopper has been battling prostate cancer and in October canceled all travel plans to focus on treatment.
He filed for divorce on Thursday in Los Angeles, citing irreconcilable differences with his wife, Victoria Duffy.
Hopper, 73, is seeking joint custody of the couple's 6-year-old daughter, Galen, and is offering to pay spousal support to Duffy.
The "Easy Rider" star last year finished shooting the second season of "Crash," a TV version of the Oscar-winning 2004 film that airs on the Starz cable network. Hopper also has several film projects in the works.
Phone and e-mail messages left for Hopper's manager, Sam Maydew, have not been returned.