Functional bone microstructure of long limb bones is a function of species-specific biomechanical properties such as locomotion and weight. Histomorphometry and statistics were used to identify various primate species (Hylobates moloch, Pongo satyrus borneensis, Pan tr. troglodytes, Gorilla g. gorilla, Homo sapiens), equid species (Equus caballus, Equus asinus, Equus mulus, Equus hemionus kulan, Equus ferus przewalskii) and also extinct horses e.g. iron age, medieval and neolithic forms on the microstructural level. Furthermore, bones from domesticated cattle, their Neolithic forms, pigs, sheep and goats (Bos taurus, Sus scrofa, Ovis aries, Capra hircus) were examined. Thin sections from proximal metacarpi or radii per species were taken in case of the domesticated animals and from distal humeri in case of the primates. Areas, perimeters, minimal and maximal axis of Haversian canals and secondary osteons were measured on digital images. Canonical discriminant analysis permits a differentiation of the species by these parameters of bone microstructure. Thus it is possible to distinguish between the different primate species, sheep and goats, horses, extinct horses, donkeys, mules and kulans on the microstructural level, however not between cattle and pig, E. f. przewalskii and Equus caballus, medieval and iron age horses. Neolithic cattle and horses do overlap, yet they are different from the modern forms.