Special Region of Yogyakarta is one of the regions that has high potential for natural disasters. Food is the most consumable material which is needed when natural disasters occur. An alternative form of food preservative is needed to maintain nutritious foods that will be distributed to the victims of natural disasters. The foods must still appropriate to eat. In this research, watermelon rind was chosen as an ingredient to make natural preservatives because they contain flavonoids and anthocyanins. This research aims were to determine the total content of anthocyanins, flavonoids and phenolics in the red watermelon rind and yellow watermelon rind, also to determine the effect of chitosan composition to the ability of flavonoids and phenolics release in the food. This research was carried out by extraction and encapsulation methods. The analysis included the content of Total Anthocyanin (TA), Total Flavonoids (TF) and Total Phenolic (TPC) in the supernatant. The other analysis was in vitro tests that was done to know the ability of flavonoids and phenolics release in the food. The total anthocyanin content in the red watermelon rind was 0.0334 mg L-1 while in the yellow watermelon rind was 0.0668 mg L-1. The total content of flavonoids in the red watermelon rind was 0.7369 g mL-1, while in the yellow watermelon rind was 0.3296 g mL-1. The total phenolic content of red watermelon rind was 0.3669 g mL-1, while in the yellow watermelon rind was 0.2273 g mL-1. In both of red and yellow watermelon rind, the highest release of flavonoid and phenolic levels showed in the variations of chitosan mass 0.4 grams. The highest flavonoid content released was 0.0638 g mL-1 in red watermelon rind and 0.0702 g mL-1 in yellow watermelon rind. The highest phenolic content released was 0.0321 g mL-1 in red watermelon rind and 0.0408 g mL-1 in yellow watermelon rind.