Genetic diversity manipulates a prime and vital role in the sustainable use of genetic resources. The data highlighted more insights into the genetic diversity of the arta plant ( Calligonum polygonoides subsp. comosum) populations collected from three localities, Qalabshu ( QQ), Mutubas ( MM) and Gamasa (GG), in Egypt as gene pool for biodiversity conservation and afforestation. Random amplified polymorphic DNA (RAPD) markers investigated the population pattern and structure. A total of 129-amplicons oscillated from 145 to 1505 bp and a total of 19-amplicons were specific markers with an average of nine bands for each population. The Shannon index (I) scored at an average of 0.3. The diversity ( h) oscillated from 0.11 to 0.25. The similarity matrices based on Jaccard coefficient recorded positive values. A higher correlation (r = 0.83) was between the combined Qalabshu (QQ) and Mutubas (MM) matrices using the Mantel test with 1,000 permutations. This species has higher adaptability for their regions. This gene pool is a valuable reservoir for enriching genetic diversity and provides basal information for the biodiversity conservation of a dominant species. The dominant species can be utilised in afforestation in the same region or another region which has the same environmental conditions.