The team did not specify why Adubato quit just before the Mystics' home game against Chicago.
"Richie felt that it was in his best interest to leave our team," general manager Linda Hargrove said.
Assistant Tree Rollins was selected as interim coach.
The Mystics were 33-39 under Adubato, who joined the team before the 2005 season, and were coming off an 18-16 mark and a playoff appearance. Adubato was the longest-tenured coach in the team's history. Before he was hired, the Mystics went through seven coaches in seven years.
The Mystics were considered the most stable team in the WNBA this offseason, with Adubato returning for a third season along with almost the entire roster from the 2006 playoff team.
But they struggled defensively during an 0-4 start, allowing opponents to score an average of 84 points.