Hayai-Annotation Plants is a browser-based interface for an ultra-fast and accurate functional gene annotation system for plant species using R. The pipeline combines the sequence-similarity searches, using USEARCH against UniProtKB (taxonomy Embryophyta), with a functional annotation step. Hayai-Annotation Plants provides five layers of annotation: 1) protein name, 2) gene ontology terms consisting of its three main domains (Biological Process, Molecular Function, and Cellular Component), 3) enzyme commission number, 4) protein existence level, and 5) evidence type. It implements a new algorithm that gives priority to protein existence level to propagate GO and EC information and annotated Arabidopsis thaliana representative peptide sequences (Araport11) within five minutes at the PC level.