CITRUS a member of the Rutaceae family, is one of the commonly cultivated fruit trees in temperate regions. The taxonomy and systematics of the genus Citrus are very complicated, and the precise number of natural species is unclear. Towards this effort, here the retrotransposable and microsatellite represent one of the most effective aspects for determination the genetic diversity in the plant genome. In the present investigation, a detailed overview of evaluating 21 LTR-REMAP and 27 SSR markers in the discriminating capacity, efficiency and ability of the genetic variability among 20 genotypes in the genus Citrus. The LTR-REMAP profile displayed 1.28 fold higher value of marker index (MI) compare to the SSR profile, highlights the distinctive nature of LTR-REMAP assay. This marker was more sensitive and provided much more evidence to discriminate at low taxonomic levels, especially for Egyptian acidic, whereas, SSR can differentiate within the group level only. Intriguingly, the heatmap cluster analysis (HCA) and principal component analysis (PCA) data drew an accurate monophyletic annotations cluster in Citreneae species, offer unambiguous identification without overlapping groups between true species and related hybrids of citrus, resulted in their placement in different clades. The use of molecular technologies will help to overcome the obstacles of cultivars identification, genetic variability in the Egyptian citrus breeding.