Food Security and Vulnerability Atlas Indonesia 2015 classified the vulnerability to food and nutrition insecurity in nine indicators covering food availability, food access and food utilization. The program was focused in 2 district (Manokwari and Merauke) in Papua region, Indonesia, from August 2015 for multi-years activities. Program was developed in cooperation between Kemendes PDTT (Ministry of Village, Development of Disadvantaged Areas and Transmigration); UGM Yogyakarta and local goverment of each District. According to the performance of vulnerability to food and nutrition insecurity, all 14 districts in priority group 1 that most vulnerable to food insecurity are all in Papua. There are five key issues related to food insecurity in Papua region, namely: Child stunting, Normative Consumption per Capita Ratio (NCPR), Percentage of people living below the poverty line, Percentage of households without access to clean and safe drinking-water, and poor families. The availability of food especially the production of rice, maize, cassava in Manokwari and Merauke were relatively less developed. The percentage of children under 5 who are more than -2 standard deviations (-2 SD) from their age and gender-specific reference heights (2005 WHO standards) were more than 40%. Based on the indicators the ratio of consumption to production in Manokwari was relatively high deficits (> 1.50) due to the limited rice area. Percentage of villages with no access to land and natural fresh water is quite low (<10%), because of large area and high presipitation in Papua. The poverty was high (25-35%) causes a low access to food, about 30-40% of households have no access to clean water directly. Manokwari and Merauke district have optimal edaphic factors (land area, vast land, not yet explored land, relatively fertile soil, ample water resources, natural, no pollution, low accessibility), optimum agro-climatic factor (high rainfall, optimum temperature, strong sunlight intensity, throughout the year), optimum potential biological factors (high biodiversity, high growth, high cultivating potential, still not intensive farming and livestock), socio-economic culture factor that is less than optimal (nature high-dependency, indigenous peoples' traditional, low population density, lack of education, high poverty, bad nutrition, natural clean water, low ethos, low resilience, low adaptability, more progressive immigrant communities). Their disaster-prone conditions will determine areas vulnerable to food. The potential of agro-ecosystems that have great potential as a major leverage to the strong regional food if managed properly. Development of master plan for food security 2015-2019 through (i) capacity building of human resources, (ii) natural resource management (iii) business management, would give smart and futuristic perpective program for food security