Animal crude drugs (natural medicines derived from animal organs) have been widely used in various Chinese medicine for the therapeutic effects and for enhancement of immunologic functions. We found the specific identification methods using DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analyses for mitochondrial DNA (mt DNA) in order to discriminate between the animal species and organs as well as the placenta of humans. Species-specific PCR bands of D-loop mt DNA for equine, bovine, porcine, and human were 133 bp, 137 bp, 231 bp, and 240 bp, respectively. Porcine organs were identified using restriction enzyme, HphI cut into two subfragments, 36 bp and 195 bp bands in the heart, spleen, and liver, except for kidney. The heart and liver of porcine were identified using restriction enzyme, SpeI cut into two subfragments, 84 bp and 147 bp bands, except for kidney and spleen. Bovine organs were cut into 68 bp and 69 bp bands in the liver, kidney, and spleen using NalIV, except heart and placenta. Placentas of bovine and humans were easily identified using each primer. Our results suggest that sequencing of mt DNA and its PCR-RFLP methods are useful for identification and discrimination of inter- and intra-specific variations in equine, bovine, porcine, and human by routine analysis.