MORTAR aims to support workflows for molecular in silico fragmentation and substructure analysis as well as the development of new fragmentation methods. The Java rich client application provides a graphical user interface for visualising the fragmentation results of individual molecular compounds or whole sets of molecules. It supports performing fragmentation with a single fragmentation algorithm or with a pipeline that can be any combination of the integrated fragmentation algorithms. Furthermore, MORTAR allows straightforward integration of additional fragmentation and substructure analysis methods.