In this work, we used 27 apple (Malus Mill.) accessions originated from China to assess the feasibility of using tailed primer M13 microsatellite markers (TP-M13-SSR)to establish genetic fingerprints and barcode technology to establish molecular identity cards of the apple collection. For the 27 accessions, twelve SSR markers resulted in the amplification of 251 alleles, with an average of 21 alleles per locus. The ranges of gene diversity, PIC and locus heterozygosity of the accessions using 12 SSR loci were 0.6620-0.9455, 0.6327-0.9211 and 0.6538-0.9319, respectively. The primer CH05b06 successfully differentiated all of the accessions. Based on the genetic fingerprints at CH05b06, we could obtain the special molecular identity cards for every accession. This technology could be used to establish genetic fingerprints and then obtain molecular identity cards for every accession, which could develop a set of reference standards for the apple collection which could be used as a database to identify unknown apple varieties.