Pecan [Carya illinoinensis (Wangenh.) K. Koch] is an important woody oil plant and a famous nut tree species, which has been widely cultivated in China. Adequate identification of different cultivars is showing the top priority in marketing. This study aimed to develop SSR markers which would be used for analyzing the pecan genetic diversity and constructing the molecular fingerprint and IDs. A total of 80 primer pairs were used for analyzing the polymorphisms in eight cultivars. Twenty-three (28.75%) SSR primer pairs from 13 chromosomes could amplify the target fragments. These primers were further used for genotyping in 45 samples of 36 pecan cultivars, such as ‘Pawnee’, ‘Mahan’, ‘Stuart’, ‘Kanza’, and ‘Shawnee’, and produced a total of 70 alleles in all samples. Eighteen primer pairs were detected with polymorphisms in different cultivars, showing the number of alleles (NA) ranged from 2 to 8, and the polymorphism information content (PIC) values from 0.03 to 0.72. The genetic distance between different cultivars ranged from 0.026 to 0.6359, and the genetic distance between samples from different sources of the same cultivar ranged from 0 to 0.0127. A dendrogram generated by the UPGMA method suggested three groups, of which group I contained 32 cultivars and most of them have the genetic backgrounds of ‘Schley’, ‘Success’, and ‘Major. Group II and Group III contained three and one cultivars, respectively. By use of (at least) five SSR primer pairs, including Ciz91, Ciz85, Ciz81, Ciz140, and Ciz107, all the cultivars were classified. These primers were selected as core SSR markers to construct molecular fingerprints and IDs. The molecular IDs were illustrated as bar codes and QR codes. Collectively, this study provided markers applicable for the cultivar identification and traceability in pecan, which has implication in the progress of pecan cultivation and production.