Mango is one of the most important fruits in Asia and the tropical and subtropical regions of the world. In this study, the intraspecific genetic variation of 30 mango genotypes (Mangifera indica L.) from some regions (Roudan, Manoojan, Faryab, Jiroft, Anbarabad, Hishin, Dehkahan and Boluk) in two southern provinces of Kerman and Hormozgan was investigated by evaluating the trnH-psbA intergenic region. After sampling the young leaves, DNA extraction was done by using dellaporta method and PCR was conducted using trnH-psbA (IGS) primers. Proliferated products of each genotype were recorded in the NCBI database after sequencing. Analysis and drawing phylogenic relationships dendrogram and sequence similarity matrix was done by using Darwin, Popgene and Mega softwares to determine genetic relationships and genetic distances between genotypes. Sequence analysis showed that in the trnH-psbA intergenic region, 361 positions were identified. Studying the sequence homology of all mango samples represented a common sequence of 116 base pairs among them. Based on the dendrogram resulted from cluster analysis, all genotypes classified in 4 groups. Based on the results, it can be concluded that the use of the trnH-psbA intergenic region was useful for studying and identifying the diversity and interrelationships of mango genotypes.