Mouflon (<em>Ovis aries musimon</em>) and sheep (<em>Ovis aries aries</em>) are considered as the wild and domestic subspecies of the same species. A comparative study on the microstructure of mouflon and sheep femoral bone diaphysis is here reported. Bone microstructure is described for the first time in the mouflon. More than 200 secondary osteons from both subspecies were analyzed and qualitative evaluation was followed by quantitative determination of perimeter, area, minimum and maximum diameters of secondary osteons and Haversian canals. The basic structural patterns observed in both subspecies can be classified as plexiform and irregular Haversian tissue, in accordance with what reported in the literature for most ruminants. The presence of many secondary osteons in the mouflon means that the bone also consists of dense Haversian bone tissue. Statistical analysis demonstrated that mouflon secondary osteons are larger than in the sheep and made of a greater number of lamellae. Since mouflon and sheep are taxonomically closely related and their body size is very similar, the qualitative and quantitative differences here reported could be primarily explained on account of their different lifestyle. Indeed, the habits of wildlife typical of mouflons may lead to the presence of wide areas of dense Haversian tissue in that subspecies, as mechanical stresses are known to be related to number and size of secondary osteons. Finally, this analysis could provide a useful tool to recognize bones from different species, in forensic exam and archaeozoological studies as well.