By Agence France-Presse
Hundreds of gunmen flying black IS flags seized Marawi in May last year, triggering a five-month battle that claimed more than 1,100 lives, in a bid to establish a caliphate in the largely Catholic country.
Nasser Lomondot was arrested on Saturday in Manila, months after he fled the fighting in Marawi.
"He participated in the killing of innocent civilians and committed violence against female and child hostages," regional military spokesman Major Ronald Suscano told reporters.
As government forces battled to wrest back control of Marawi, Lomondot directed a diversionary attack by pro-IS gunmen in the neighbouring town of Marantao, Suscano added.
"He was one of the key planners of the attack in Marantao town ...while the firefight was still ongoing" in Marawi, Suscano said.
Lomondot was arrested with a second pro-IS suspect, Manila police chief Oscar Albayalde said in a statement.
The Philippine military warned last month that the remaining militants from Marawi have mustered a force of about 200 gunmen to launch a second attempt to put up a caliphate in the country's south.