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The soil mantle of the tropical karst landscapes of southern Mexico was a key resource for ancient Maya agriculture and experienced deep transformation due to long-term human impacts under changing environmental conditions. We conducted a comparative analysis of three compound soil toposequences in mountainous (Sierra de Chiapas/Middle Usumacinta Valley, Busiljá, and Chinikihá archaeological sites) and platform (NE Yucatán Peninsula, Yalahau region) karst landscapes to reconstruct general tendencies and regional variations in pedodiversity development and soil–human interactions since the Early Preclassic Period. Toposequence characterization is based on macro- and micromorphological observations, accompanied by a suite of laboratory data. Calcareous upland geoforms of all toposequences have similar soil combinations consisting of shallow Rendzina and deep red clayey Terra Rossa types of profiles. We argue that Rendzinas, now dominant in the upland soil cover, in most cases, are not a product of incipient pedogenesis on limestone; they have developed from the residues of Terra Rossa soils after their advanced erosion. Pedosediments generated by ancient soil erosion have been found in the piedmont and depression positions in the mountainous landscapes of Chiapas, as a result of lateral downslope soil removal, and in the subsurface karstic cavities in the platform of NE Yucatán, indicating vertical “soil piping.” The soils of the lowland domains show contrasting differences between the toposequences: gleyic clay–rich soils and humic alluvial soils prevail in Chinikihá and Busiljá, whereas hydromorphic carbonate soils have formed in Yalahau karstic depressions. These differences in the lowland soil properties led to divergent ancient Maya land use strategies; in Chinikihá and Busiljá, the major agricultural domain was developed in the lowlands, implying largescale artificial drainage. On the contrary, in Yalahau, mostly upland Rendzinas were cultivated, implying “precision agriculture” and “container gardening.”