Abstract Summary Here, we introduce YeastMate, a user-friendly deep learning-based application for automated detection and segmentation of Saccharomyces cerevisiae cells and their mating and budding events in microscopy images. We build upon Mask R-CNN with a custom segmentation head for the subclassification of mother and daughter cells during lifecycle transitions. YeastMate can be used directly as a Python library or through a standalone application with a graphical user interface (GUI) and a Fiji plugin as easy-to-use frontends. Availability and implementation The source code for YeastMate is freely available at https://github.com/hoerlteam/YeastMate under the MIT license. We offer installers for our software stack for Windows, macOS and Linux. A detailed user guide is available at https://yeastmate.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.