This study examines the spatial organization and long-term development of two ancient Maya centres Lagartera and Margarita located in south-central Quintana Roo, Mexico, that were occupied from the Middle Preclassic (ca. 500 B.C.) to the Terminal Classic (ca. A.D. 1000). Archaeological research at these two sites was designed to investigate the socio-political factors responsible for their different layouts. Spatial data, obtained through survey and mapping, and chronological data, obtained through excavations, were used to identify patterns in the built environments and to reconstruct the history of occupation of each site. By comparing the layout, composition, temporal development, and regional context of Lagartera and Margarita, this study highlights various dimensions of variability among ancient Maya centres and discusses the sources of this variability.