In this paper data concerning the taphonomy of the Upper Pleistocene site Aghia Napa in Cyprus is presented. The site is dominated by skeletal material belonging to the pygmy Hippopotamus species Phanourios minor, and consists a littoral rockshelter. The fossiliferous assemblage is spread in a total area of about 72 m2 and a significantly large number of specimens were collected, indicating the presence of more than 160 individuals at the site. In this paper, we attempt to identify the causes or mechanisms that led to the accumulation of the endemic hippopotamus remains, focusing also on the palaeo-environmental parameters that might had affected the survivorship of the fossils. The taphonomical analysis is also based on parameters, which provide information concerning skeletal element representation and thus survivorship. The study of the skeletal material shows signs of abrasion, cracking and significant fragmentation which are related to the type, size and shape of the skeletal elements. The bone assemblage is interpreted as a result of transportation of the skeletal material from longer or shorter distances in the surrounding area while the impact of man concerning their accumulation is still under discussion.