The aim of this study is to investigate the molecular identification of the Iraqi truffles species and a better understanding of genetic diversity in the center of the truffles habitat. Thirty-two samples were collected from the Iraqi desert and local markets. Samples were chosen depending on the morphological diversity of the fruit body and sample collection area. Results of ITS region sequencing for the 32 samples showed two genuses Tirmania and Terfezia are the main dominant, 4 species of Tirmania pinoyi and 28 species of Terfezia claveryi. All species sequences were deposited in NCBI GenBank and all had accessions number. The neighbor-Joining method was used to generate a phylogenic tree to study the genetic diversity of the ITS sequences for the 32 Iraqi truffle samples. Results showed a high genetic diversity for the Iraqi truffles samples. The phylogenic study showed Iraqi truffles clustered with different groups as a clade with the reference sequences from other countries represent three continents Asia, Africa, and Europe. Also, we found in this study a unique cluster group for the Iraqi sequences for T. pinoyi and T. claveryi truffles cluster in one group and do not match with any reference sequences used in this study. This is a piece of strong evidence proofed the Iraqi habitat could be the origin of center diversity for the T. pinoyi and T. claveryi truffles.