In the current study, ramp-PCR fragments from improved RAPD (random amplified polymorphic DNA) amplification of Lycium (Goji) species or cultivars were cut and cloned into the vector of pGEM-T. A positive clone 10–5 was screened by PCR amplification, enzymatic digestion, and Sanger sequencing. A SCAR (sequence-characterized amplified region) marker, named Goji 10–5, with 949 nucleotides in length, was identified. Goji 10–5 is specific to Goji species Lycium chinense Miller from Jiangxi in China and Texas in the USA. A BLAST search of this nucleotide sequence in the GenBank database indicated that it shows no identity with any other species, including no any other Lycium species. As a new sequence, we have deposited it in the GenBank database with accession No. MN862323. PCR assays were developed and converted the nucleotide sequence to become a novel molecular marker for Lycium chinense Miller, named Goji 10–5. This marker may be used for the genetic identification of other samples. This study has successfully developed Goji 10–5, a specific SCAR marker to identify L. chinense and distinguish it from other species, including other Lycium species from different locations.