The article introduces MISA-web, a web-based application that extends the functionality of the MISA microsatellite finder tool. MISA-web addresses two major limitations of the original MISA: the need for computational expertise and the proprietary output format. The new tool is designed to be user-friendly and supports both the proprietary MISA output format and the widely used GFF3 format for downstream analysis. The workflow involves monitoring server load, processing user inputs, running MISA, and sending results via email. The performance of MISA-web is validated against other microsatellite detection tools using barley bacterial artificial chromosome (BAC) sequences, demonstrating its effectiveness and comparable execution time. The GFF3 output format enhances integration with downstream analysis pipelines. The development of MISA-web was supported by the German Federal Ministry of Education and Research.The article introduces MISA-web, a web-based application that extends the functionality of the MISA microsatellite finder tool. MISA-web addresses two major limitations of the original MISA: the need for computational expertise and the proprietary output format. The new tool is designed to be user-friendly and supports both the proprietary MISA output format and the widely used GFF3 format for downstream analysis. The workflow involves monitoring server load, processing user inputs, running MISA, and sending results via email. The performance of MISA-web is validated against other microsatellite detection tools using barley bacterial artificial chromosome (BAC) sequences, demonstrating its effectiveness and comparable execution time. The GFF3 output format enhances integration with downstream analysis pipelines. The development of MISA-web was supported by the German Federal Ministry of Education and Research.