Notarchirico is at a nodal point in time and space for understanding the settlement of Europe in terms of migration or in situ evolution. Former technological analyses have not shown significant differences between the different lithic assemblages at Notarchirico. Our approach here is to produce a phylogenetic analysis of the lithic assemblages taken as the terminal of the analysis and interpreted as cultural units. In the cladistic framework, characters are hypotheses of relationships between lithic assemblages, and homologies are hypotheses of relationships between lithic objects; cores, flakes, nodules. To effectively grasp informative lithic innovations in the assemblages, we formalise cladistic hypotheses as hierarchical characters in the framework of three-item analysis, and propose a new algorithm to remove the high number of repeated terminals among trees inherent to a cladistic analysis of assemblages. Beyond the classic distinction of the presence or absence of bifaces, our analysis of the five Notarchirico layers, dated between 670 and 700 ka, highlights a well-supported cladogram grounded on complex hierarchical characters on lithic artefacts. This cladogram shows a paralogy event between the flakefree layer H, representing short-term occupancy, and the other layers representing long-term settlements. The resulting cladogram shows that relationships between lithic assemblages at Notarchirico do not follow the stratigraphy. Moreover, the Notarchirico lithic assemblages cannot be explained in an entirely local way, but seem to be part of a more complex European history.