Biodiversity is closely related to the conservation of ecosystems. Ecosystems provide more subtle, but equally essential, services. Microorganisms decompose human's waste and renew the soils that produce our food crops. Biodiversity in Korean paddies encompass 54 families and 107 species of freshwater invertebrates. In terms of the number of aquatic insects affected by different sources, the order starting with the highest population was swine slurry > chemical fertilizer > fresh straw with reduced fertilizers > control. The number of freshwater invertebrate and aquatic macro-invertebrate in surface water of the plots without insecticidal application were 2 and 2.1 times greater than in fields receiving insecticide applications, respectively. The soil microfungal flora of the 85 isolates paddy fields in Korea was 30 species in 13 genera and 11 isolates were unidentified yet. Agricultural policy should be changed to assist the conservation of biodiversity because until now the agricultural ecosystems have been negatively affected from the development of high-yield varieties to enhance food production, and the expansion of fertilizer and chemical use. For the conservation of agricultural ecosystems, agricultural practices with less investment and more resource saving, as well as enhancing the safety of agricultural and livestock products are essential. Finally, this paper was written for the contribution for the development of environmentally friendly farming systems with neighboring or whole ecosystems.