Military chief Gen Emmanuel Bautista says Communist Party of the Philippines chairman Benito Tiamzon and his wife, Wilma, who is also a senior party officer, were arrested today in central Cebu province.
The arrest comes a week before the party's armed wing, the New People's Army, marks its 45th anniversary.
Bautista says the couple faces charges of crimes against humanity, including multiple murders.
Bautista is calling on the rebels to abandon their armed struggle.