This study examined the Integration Program of the Philippine Government for former MNLF members into the AFP, particularly in Basilan and Zamboanga. Its aim is to bring former fighters to the mainstream of society and to promote peace and order in Mindanao. The objectives are to determine how the GRP and the MNLF implement provisions of the JPA and examine the awareness of the recruits; and to find out problems encountered by the integrees before, during and after their integration to the AFP. Descriptive method was used through FGD, KI interviews, and passive observation. Questionnaire checklist was utilized for sociodemographic profile. The sixty five respondents answered that the greatest problems prior, during and after integration were the following: enforced integration, unfair distribution of quota, no clearcut qualifications and lack of proper dissemination of information; no assistance to education and fixed monthly salary; unclear instructions, bureaucratic system; complicated mental training, discrimination, abuse of authority by the trainers; not permitted to go home, and low quality firearms; fake MNLF fighters, bribery; no respect for religious beliefs and discrimination from the PA; delay of salary, unfair release of coupon and mess, no scholarship for EM and no implementation of livelihood programs. Majority of these problems are structural in nature with primary attitudinal problems and it is to understand that with these problems there is a great need to rediscover the values of cultural solidarity and to reemphasize the positive and relevant roles that each should take to achieve a lasting and relevant national commitment for peace. Keywords - Peace and Order, Moro National Liberation Front, Armed Forces of the Philippines , Government of the Republic of the Philippines, Descriptive Method, Basilan and Zamboanga, Philippines,