In this study, a coupled thermodynamics and crankshaft dynamics model of a large two-stroke diesel engine was utilised,to map the relationship of the engine Instantaneous Crankshaft Torque (ICT) with the following frequently occurring malfunctioning conditions: (a) Change in Start of Injection (SOI), (b) change in Rate of Heat Release (RHR), (c) change in scavenge air pressure, and (d) blowby. This was performed using frequency analysis on the engine ICT, which was obtained through a series of parametric runs of the coupled engine model, under the various malfunctioning and healthy operating conditions. This process demonstrated that engine ICT can be successfully utilised to identify the distinct effects of malfunctions (c) or (d), as they occur individually in any cylinder. Furthermore, by using the same process, malfunctions (a) and (b) can be identified as they occur individually for any cylinder, however, there is no distinct effect on the engine ICT among these malfunctions, since their effect on the in-cylinder pressure is similar. As a result, this study demonstrates the usefulness of the engine ICT as a non-intrusive diagnostic measurement, as well as the benefits of malfunctioning conditions mapping, which allows for quick and less resource intensive identification of engine malfunctions.