Phytoliths, unlike pollen and charcoal, are frequently conserved in sediments in the Maya lowlands but are rarely used as paleoenvironmental proxies. To better interpret and reconstruct paleoecological signatures and changes, it is necessary to provide current analogues of fossil assemblages. To do so, we selected six modern ecosystems and differentiated them by their soil phytolith assemblages in the ancient Maya city of Naachtun (northern Petén, Guatemala). We studied the plant communities and relative phytoliths frequencies in surface soils on four north-south vegetation transect, composed of 43 quadrats. These transects cross forests and savannahs in low swampy areas North and South of the site, and hill forest in its center, where the city was built. Quadrats were statistically compared using multivariate analyses (CA). Six types of plant communities were characterized by their phytolith assemblages, as well as on the presence of siliceous bioindicators such as diatoms and sponges. The D/P and LU indexes developed for these assemblages allow us to provide a precise signature of the current vegetation cover, and identify the presence of undergrowth in forest areas, or forest edges in savannah areas. This first modern phytolith reference for the Maya area will contribute to the development of paleoecological reconstructions for this zone.