Paddy field is highly important agro-ecosystems for biological conservation. However, modern agricul-ture, which relies heavily on synthetic fertilizer, pesticide, and herbicide, can lead to several ecological problems including the loss of biodiversity and corresponding decline ecosystem service and function. Organic farming is considered an environmentally friendly method of cultivation and the most promis-ing way to overcome the negative effects of modern farming. However, as few studies have examined the advantages of organic paddy fields, investigations are necessary to determine the effects of organic and conventional methods on the biodiversity of aquatic and terrestrial organisms. Field researches will be conducted to understand the biodiversity in organic and conventional paddy fields. The 10 pairs or organic and conventional paddy fields were selected in Yogyakarta. Yogakarta is located in a fertile agricultural area with approximately 80% of the agricultural area is domi-nated by paddy fields. From this study, can understand the biodiversity indicator and the interaction among organisms within and be-tween aquatic and terrestrial ecosystem which thereby might support the ecosystem proses including nutrient cycling and pest control to achieve sustainability of the paddy field system and rice production. Moreover, the result of this study might help Indonesian farmer to understand the important of the biodiversity conservation in agriculture.