During the Late Pleistocene, Mexico had a richer fauna than today with many different forms of megafauna that are now extinct. However, the ecosystems they inhabited and the particular ecological niches that they occupied are still poorly understood. Most of the findings of Pleistocene megafauna have been in alluvial deposits that present rich opportunities for paleoecological studies using paleopedological records. Floodplain paleosols commonly are poorly developed. However, micromorphological analysis provides information about the grade of development of the soil at a microscale, discriminating between genetic and sedimentary processes; thus helping in the identification of the environmental setting in which they formed. We analyzed the micromorphology of six pedogenetic units in the sequences of Santa Cruz Nuevo and Axamilpa, in the south of Puebla, and Huexoyucan, in the state of Tlaxcala. These pedosequences correspond to the second half of marine isotopic stage 3 (MIS3), MIS2 and the early Holocene. All studied units are characterized by strong pigmentation with dark humus. The micromorphological analysis of MIS3 paleosols reveals aquatic conditions with evidence of freshwater biota and microlamination as well as pedogenetic features of hydrogenic carbonate precipitation and redoximorphic processes. The dark paleosols of MIS2 and the early Holocene demonstrate signs of stronger coprogenic aggregation, weathering and fewer gleyic features. Comparison with modern soils shows that the latter were formed under better-drained, aerated conditions that exclude redoximorphic processes. We conclude that the dark colored Pleistocene paleosol units are indicative of different paleo-landscapes: wetlands in the MIS3 and moist meadows in MIS2 – early Holocene. The swampy ecosystems could play an important role as a megafauna habitat.