Rodolfo Garcia, a former vice chief of the Philippine military, was appointed by the government of President Gloria Macapagal- Arroyo after a former negotiator quit last week.
"We know him very well from his stint as army officer in central Mindanao up to his becoming a member of the government peace panel," said Muhammad Ameen, chairperson of the MILF secretariat, in a statement on an MILF website.
Ammen also said Garcia knows Mindanao very well as well as the "nuances" of the present peace talks.
Despite a standing 2001 truce, peace talks between government and MILF hit a block last year over issue of ancestral domain and dispute over how many villages should be controlled by MILF in Mindanao.
MILF is estimated to have some 10,000 armed members and is the biggest separatist group in the country.
Malaysia has deployed a truce monitoring team in the southern Philippine region and has been hosting talks between government and MILF in Kuala Lumpur.