Bone accumulation in Palaeolithic archaeological sites is often the result of activities carried out by hunter-gatherer groups. Cultural choices may have influenced prey representation in archaeological assemblages, distorting their palaeoecological meaning. We present a comparison between large mammal and small mammal assemblages from the Upper Palaeolithic sequence of Grotta Paglicci (Apulia, southern Italy) that extends from the Marginally Backed Bladelet Aurignacian (about 39,000 cal yr BP) to the Final Epigravettian (about 13,000 cal yr BP). At Paglicci, the high frequency of horse and ibex remains indicates open and dry environments for most of the Upper Palaeolithic. This is confirmed by the predominance of the common vole among small mammals. The alternation between horse and ibex, which takes place during the Upper Palaeolithic, however, looks to be more related to variations in hunting territories. Taxon frequencies change abruptly at 17,955–16,696 cal yr BP, with an increase in woodland-related ungulates together with micromammals, indicating a climatic evolution towards milder and more humid conditions. Results demonstrate that when the association of ungulate taxa is considered as a whole, it has a good palaeoecological signal, whilst considering taxa separately can help to better understand cultural choices of past hunter-gatherer communities.