Abstract: Agricultural germplasm resources are the material basis for agricultural research and the strategic resources for the survival and development of human society. Fujian Academy of Agricultural Sciences has established 3 national/provincial germplasm resource banks, 3 national germplasm resource nurseries, 1 provincial germplasm resource nursery and 18 college-level germplasm resource nurseries. There are 38 212 copies of crop germplasm resources from 58 species, 47 567 copies of agricultural microorganisms from 646 species, 327 copies of medicinal plant resources from 45 species, 15 copies of livestock and poultry germplasm resources from 4 species, and 4 copies of aquatic germplasm resources from 1 specie. Through analyzing the problems existing in the protection and utilization of germplasm resources in Fujian Academy of Agricultural Sciences, some suggestions on strengthening the protection and utilization of agricultural germplasm resources were put forward, which was of great significance for enhancing the innovation of germplasm resources and promoting the agricultural supply-side structural reform in Fujian Province.