During the excavation of Rego da Murta Dolmen I, a structure belonging to a megalithic cluster in central Portugal, a number of small sub-quadrangular quartzite stones were found embedded within a layer below that of the deepest orthostat. In this paper, we report on these findings and highlight three key features of these small stones, namely their location relative to the dolmen’s plan, the distances between them, and their orientations. We suggest the quartzite stones could have been markers used in the planning of this megalithic structure. In addition, we analyse the orientations of the two main structures of the cluster (Dolmen I & Dolmen II), which are reflected by the orientation of the quartzite stones. We tentatively suggest potential landscape and skyscape alignments for their orientations, including three hypotheses for the observed differences in orientation between the two.