The Arabidopsis thaliana phenome is the whole set of characteristics expressed in response to genomic, environmental and experimental factors of the most major experimental plant. The huge variety of published data have been accumulated, which is an indispensable resource to improve plant omics studies both on basic and applied research fields. It is also important to link information of bioresources such as mutant lines to the phenome to improve experimental research. Inconstancy among them however has inhibited their effective application. We developed the new Arabidopsis Phenome Database integrating two novel databases. One is the “RIKEN Phenome Integration of Arabidopsis Mutants”, that allows researchers to search mutants developed in RIKEN according to their interests in specified phenotypes to find useful materials for their experimental research. The other, the “Database of Curated Plant Phenome” focusing on the Arabidopsis phenome collected by human curation of published papers, is designed to realize easily both phenotype-to-genome and genome-to-phenotype association studies.