The study of two caves from the Serra do Ramalho region is here presented, this is one of the most important karstic areas in Brazil. A taxonomic analysis revealed 29 taxa including Xenarthra, Cetartiodactyla and Carnivora, ranging from Late Pleistocene to Early Holocene. Taphonomic studies reveal taphocoenosis consisting mainly of complete elements, without significant transportation, but also of transported elements, composing spatial-mixed, predominantly in situ-preserved assemblages. The predominance of Xenarthrans found within the caves is probably biased by a taphonomic pattern since these animals would have life habits related to cave environments, therefore with higher chances of preservation. There is evidence of accidental death of the scelidotheriines in Lapa dos Peixes cave, where entrapment of the animals during one or more events of river flooding is pointed as a hypothesis. Deposition took place within different periods of dry and humid climate incorporating bones in clastic and chemical deposits. Cycles of sedimentary deposition and reworking (erosion) may have acted in generating complex and overlapping depositional patterns with time averaging. During depositional phase, while the cave environment was occupied rather by Xenarthrans, parts of other animals were transported in the scope of fluvial systems and gravity loads, as well as by accidental falling or scavengers. The sedimentary deposits are currently being eroded by rain runoff in both caves, causing the reallocation of finer sediments to deeper conduits but the fossils keep close to their original location. This process is exposing a large amount of fossils, allowing extensive sampling which would be impossible with active excavations, since it would require an excessively longer time and damages to the caves.