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Taiwan is a subtropical-tropicalisland characterized by high temperature and heavy rainfall. Intensive agriculturalpractices have served as a strong foundation for Taiwan's commercial and industrial economic miracle. In recent years, chemicalpesticides and fertilizers are extensively applied to obtain highercropyield. Overusingagrochemicals leadedto several agricultural problems and poor cropping systems.Such as theexcessive applicationof chemical nitrogen fertilizer not only acceleratedsoil acidification but also riskedcontaminating groundwater and the atmosphere. Using organic fertilizers and bio-fertilizers offersa safe option for reducing the agrochemical inputs. Bio-fertilizers are being developed in several laboratories of Taiwan overthe years. Beneficial microbesused as the candidates of bio-fertilizers including rhizobium,associative and free living nitrogen-fixing bacteria, phosphate-solubilizing bacteria(PSBs),arbuscular-mycorrhiza (AM) fungiand organic materials degrading microorganismsare continuously being isolated from various ecosystems and their performancesin laboratoriesand field conditions are assessed. The extensive research program over the years on beneficial bacteria and fungi has resulted in the development ofwide range of bio-fertilizers, which not only fulfilledthe nutrient requirements of crops,but also increasedthe crop yields. Many experiments in greenhouses and in field conditions have revealed that a different crop responded positively to microbial inoculations. In particular, successful rhizobial inoculants were applied to leguminous plants and AM fungi for muskmelons in order to increase the yield and quality. Multifunctional bio-fertilizers were developed to reduce about 1/3-1/2 of chemical fertilizer application. Enhancement and maintenance of soil fertility through microorganisms will be an important issue in future agriculture. Long-term conservation of soil health is the key benefit of bio-fertilizers, which in other words is the most sustainable form of agriculture.