ath-isomiRdb is an Arabidopsis thaliana miRNA expression database curated from raw miRNA-seq datasets sourced from the NCBI Sequence Read Archive. A comprehensive set of 2,757 samples has been uniformly analyzed using the IsoMiRmap tool, incorporating Arabidopsis thaliana miRNA data from miRBase (release 22.1). To enhance sample annotation, metadata from NCBI SRA has been seamlessly integrated. This resource stands as the first integrative repository, housing both the sequence and expression data of 20,764 Arabidopsis thaliana isomiRs. ath-isomiRdb goes beyond mere expression data, providing additional insights into isomiR targets, tissue specificity, and trait associations. All data is freely accessible in the Downloads section, facilitating seamless exploration and utilization. For any issues, queries, or requests, we encourage you to visit our GitHub page, where our team remains readily available to assist you.