MicroRNAs(miRNAs)are important regulators of gene expression.The large-scale detection and profiling of miRNAs have been accelerated with the development of high-throughput small RNA sequencing(sRNA-Seq)techniques and bioinformatics tools.However,generating high-quality comprehensive miRNA annotations remains challenging due to the intrinsic complexity of sRNA-Seq data and inherent limitations of existing miRNA prediction tools.Here,we present iwa-miRNA,a Galaxy-based framework that can facilitate miRNA annotation in plant species by combining computational analysis and manual curation.iwa-miRNA is specifically designed to generate a comprehensive list of miRNA candidates,bridging the gap between already annotated miRNAs provided by public miRNA databases and new predictions from sRNA-Seq datasets.It can also assist users in selecting promising miRNA candidates in an interactive mode,contributing to the accessibility and reproducibility of genome-wide miRNA annotation.iwa-miRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience.With flexible,interactive,and easy-to-use features,iwa-miRNA is a valu-able tool for the annotation of miRNAs in plant species with reference genomes.We also illustrate the application of iwa-miRNA for miRNA annotation using data from plant species with varying genomic complexity.