Abstract: Cross breeding is the main method of walnut breeding at present. In order to identify the authenticity of cross offspring and accelerate the process of cross breeding quickly and effectively, the microsatellite marker was used to assist walnut paternity identification. In this study, 12 microsatellite loci with relatively high polymorphism and stable amplification were selected from 60 published SSR primers of walnut. The 159 offsprings from 5 hybrid combinations were identified by genotype elimination and maximum likelihood method. The correct parents of 121 progeny were identified by genotype elimination, the identification rate was high, and the total identification rate was 76.10%. The maximum likelihood parental analysis showed that 12 offspring with unknown parents reached the confidence interval predicted the correct parents, and the total identification rate was 7.55%. There were 19 progeny whose parents were correct when the confidence interval was reached, and the overall identification rate was 11.95%. The overall identification rate was low.