Genetic analysis of short tandem repeat (STR) loci using non-invasive fecal samples is currently the most widely used method in genetic surveys of giant pandas (Ailuropoda melanoleuca). However, Low-quality fecal DNA obtained from fecal samples may affects the correctness of short tandem repeat (STR) genotyping results and poses a challenge to accurately identify individuals. The aim of this study was thus to compare the efficiency of DNA extraction kits in obtaining high-quality fecal host DNA from giant panda fecal samples. In the present study, six commercial kits widely used in fecal DNA extraction, the QIAamp Fast DNA Stool Mini Kit (Q kit), Beaver Beads™ Stool DNA Kit (H kit), Mag-MK Soil & Stool Genome DNA Extraction kit (S kit), Magnetic Soil And Stool DNA Kit (T kit), E.Z.N.A™ Mag-Bind Stool DNA Kit (O kit) and Mag Beads Fast DNA Kit for Feces (M kit), were compared to improve the efficiency of STR genotyping of giant panda fecal DNA samples. Fecal DNA concentration and purity were measured, and STR genotyping was performed using blood and fecal DNA from captive giant pandas to compare the genotype matches at 11 STR loci. Our results show that the most efficient extraction kits were the Q and T kits, and the Q kit had a greater ability to remove PCR inhibitors than other kits. However, different STR genotyping systems require different DNA extraction kits in order to achieve the highest possible genotyping correctness.