In papers filed at the Lake County courthouse, the couple said their decision to divorce after 17 years of marriage was mutual and amicable, the Chicago Tribune reported.
The two have lived apart since February. They are seeking joint custody of their three children, ages 18, 16, and 14, court filings show.
Court documents cite irreconcilable differences, and say the Jordans have agreed to a settlement on issues including property and debt, child custody and support, and parenting time, the newspaper said.
The couple issued a statement announcing the filing but declined further comment.
They asked the court to excuse them from attending a required parenting education program class because, they said, their celebrity "would be a disruption to the class" and would "create publicity" about their personal and private issues."
Juanita Jordan filed for divorce in January 2002, but withdrew the petition after one month when the couple said they would try to reconcile, the newspaper said.
Michael Jordan, 43, is part owner of the Charlotte Bobcats. He played in six NBA champion Chicago Bulls teams.