This work presents an open Java rich client Graphical User Interface (GUI) application, abbreviated MORTAR (MOlecule fRagmenTAtion fRamework), with the intention to support the development of new in silico molecule fragmentation algorithms as well as enable their later distribution in a more accessible way. Its main functionalities are importing molecule sets from various file formats, applying fragmentation algorithms, and visualising the results in a graphical display that alleviates the investigation of the resulting fragment sets and the fragmentation results of individual molecules. Using MORTAR, no programming skills are needed to perform these steps, which makes conducting in silico fragmentation studies more accessible. MORTAR can be installed and used on three major operating systems (Windows, macOS, and Linux) and uses parallel computing on multi-core processors for CPU-intensive processes. To our knowledge, there is currently no comparable open software application available. For cheminformatics functionalities, the Chemistry Development Kit (CDK) is employed internally. Fragmentation algorithms can be integrated into or directly developed in MORTAR straightforwardly. Upon release, three algorithms are available: The Ertl algorithm for functional group identification via its open implementation ErtlFunctionalGroupsFinder , the Sugar Removal Utility for glycosidic moiety detection and removal, and Scaffold Generator , a software library for scaffold functionalities, including the scaffold tree dissection into parent scaffolds and an enumerative parent scaffold generation routine for scaffold networks. More functionalities will be added in future releases and with MORTAR being open-source, the software itself can be enhanced or tailored to individual needs.