Geometric morphometric techniques may offer a promising methodological approach to analyze evolutionary novelties in a quantitative framework. Nevertheless, and despite continuous improvements to this methodology, the inclusion of novel features in these studies presents some difficulties. In the present study, different methods to explicitly include novel traits in geometric morphometric analyses are compared, including homology-free approaches, landmark-based approaches, and combinations of both techniques. The two-dimensional occlusal morphology of the lower second molar in multiple hominin species was chosen to evaluate these methods, as an example of an anatomical structure including one novelty: a distal fifth cusp is present in earlier hominins, and notably absent in many later Homo species. Results reveal that different approaches provide different results, highlighting that the design of the conformations of landmarks has a high impact on the inferred conclusions. Among diverse methods, a combined approach including landmarks, sliding semilandmarks, and only one landmark related to the studied novelty (an indicator of its absence or presence and of its size, when present), was able to directly discern structures with and without the novel feature, circumventing some of the methodological difficulties associated with these traits. This study demonstrates the ability of geometric morphometric techniques to investigate evolutionary novelties and explores the implications of different methods, providing a reference context for future studies.