The difficulty of distinguishing different taxa of equids from one another on the basis of skeletal morphology has led to the search for alternative means by which archaeologically recovered bones may be separated according to species or hybrid. Protein radioimmunoassay (RIA) offers much promise in this regard because it identifies specimens using constituent proteins that differ from species to species and that tend to blend in selectively bred crosses. The method works for ancient bones only when sufficient amounts of the appropriate proteins survive. Bone samples were assayed from wild, hunted onagers recovered from Neolithic levels of Ali Kosh Tepe in lowland southwestern Iran and from possible hybrids recovered from Bronze Age levels of Godin Tepe in highland western Iran. Although insufficient albumin remained with which to accomplish the intended goal of species identification, the pattern of collagen retention provided important information on the relationship between taphonomy and protein survival.