Abstract: The genotyping-dendrogram of short tandem repeat (STR) has been established based on near-infrared spectroscopy in combination with the principal discriminate variate method. Six genotypes 9-9, 9-11, 9-12, 10-10, 10-11 and 11-11 of D16S539 locus, which had different total number of core-repeat units and the high frequencies of occurrence, were selected as the research objects. The samples of 6 genotypes were obtained by polymerase chain reaction (PCR) in twice. Discriminate models with the near-infrared spectrum of each PCR product as discriminating variable were built. Based on the differences of total number of the core-repeat units, the genotyping-dendrogram was established. It was shown that these models in the dendrogram were appropriate for discriminating the genotypes of all the samples and the method was of good stability and predicting ability. It provided potential to establish expert system for genotyping of other STR loci.