Forty-one years had come and gone since the Philippine Catholic hierarchy hosted the First National Congress for Rural Development with the theme ―Man and Land in the Philippines in the Light of Vatican II‖ on February 5 to 11, 1967. It is good to review the proposals presented then by the delegates who had offered much hope for the poor and the rural folks. Much of these proposals were translated into action which made impact on the lives of the very poor. In July 2007, the Catholic Bishops Congress of the Philippines (CBCP) Plenary Assembly approved the organizational structure of the National Rural Congress (NRC) II and the timetable of activities. Phase One consisted of two parallel local-level consultations. Diocesan (ad intra) consultations on the role of Basic Ecclesiastical Communities (BECs) in rural development were undertaken by the National Secretariat for Social Action (NASSA), the Episcopal Commission for Indigenous Peoples (ECIP), and the BEC offices. Here in the Mindanao Region, the Ad Intra consultations were conducted in majority of the 21 dioceses spread throughout at the level of the Basic Ecclesial Communities (BECs). Sub-regional (ad extra) consultations for Mindanao were focused on the different basic sectors facilitated by the different non-government organizations (NGOs) and peoples’ organizations (POs) and the data were collated by a research team (based in Xavier University, Cagayan de Oro City) using the sub-regional focus. After the conduct of the consultations, the data generated were forwarded to the Congress Secretariat and were collated and interpreted by a research team composed of three member institutions of Davao Association of Colleges and Schools (DACS) namely the San Pedro College, Holy Cross of Davao College, and the University of Immaculate Conception. Based on the collated study reports (ad intra and ad extra) and the documented reactions of the congress participants, the root cause of the problems in Mindanao is the national governance. The problem with governance in return has resulted in environmental degradation; deadly health care system; displaced population and dysfunctional families; discrimination and violation of the rights of indigenous people; inadequate and substandard infrastructural projects; government’s deceitful practices, culture of corruption, lack of trust and lack of political will; the deteriorating state of education; escalation of violence and growing incidence of criminality; and government’s inaction or inefficient action on livelihood. The study identified four priority issues in Mindanao: the application of real land reform; protection of the rights of the indigenous people; morally credible governance; and the elimination of development aggression in the environment.