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We describe and analyze the mineralogical, geochemical and paleohistological characteristics present in hemimandibles of Paedotherium bonaerense (Ameghino) (Mammalia, Notoungulata, Hegetotheriidae). Remains were recovered from floodplain deposits of the Monte Hermoso Formation (early Pliocene). Francolite is the main mineral component in all hemimandibles, evidencing compositional changes in the internal crystalline structure during fossil-diagenesis. The similarity in the chemical composition of the fossils and the hosting rocks suggests that the enrichment of the remains with new elements was due to direct exchange with the sediments in which they were buried. Original bone microstructure shows good preservation, only affected by permineralization and microfissures. Manganese and iron oxides are the most abundant minerals infilling microstructural features and microfissures. The dark color identified on the outer surface of some remains is related to precipitation of manganese oxides. The results obtained allow us to establish the processes affecting the remains before and after burial, and thus interpret the different taphonomic histories. This work provides new information on a issue usually not considered in studies on vertebrate communities from the South American Neogene and at the same time it establishes a framework for the analysis of assemblages with similar characteristics.