Carbonate rocks of lower Permian age are important host to copper skarn mineralization, in the porphyry copper belt of southeastern Arizona, near Tucson. Early Permian sedimentation occurred on an unstable shelf with abrupt facies changes, resulting in diverse lithologies, repetitive depositional sequences and obscured formational contacts. Favorable carbonate protoliths are not necessarily confined to a given stratigraphic horizon, nor limited to a particular formation, complicating efforts to determine stratigraphic controls of skarn mineralization within a porphyry system. Since carbonate rock types are defined by their depositional environment, facies modeling may help to delineate important carbonate skarn protoliths, in altered section. This study represents a synthesis of previous work, and adds new observations and stratigraphic interpretations of the lower Permian Earp, Colina and Epitaph Formations within the porphyry copper belt of present day Pima and western Cochise Counties, Arizona. Potentially favorable carbonate protoliths are described, utilizing stratigraphy and facies analysis as a means of determining their spatial distribution. For workers studying altered drill core associated with copper mineralization, important diagnostic features of lower Permian protoliths and marker beds useful in altered section are discussed here, along with their commonly associated skarn assemblages.