Background: Phylogenetic analysis is widely used to determine the evolutionary relationships, and it is expressed by the phylogenetic tree. The current work aimed to identify the phylogenetic tree of Egyptian and Iraqi population samples, and to compare between the used deoxyribonucleic acid (DNA) fingerprinting techniques [Inter-Simple Sequence Repeat (ISSR)- polymerase chain reaction (PCR) and Random Amplified Polymorphic DNA (RAPD)-PCR]. Methodology: This comparative cross-sectional study was carried out on 48 unrelated healthy volunteers from different geographic areas [Northern Egypt “NE”, Southern Egypt “SE”, Northern Iraq “NI” and Southern Iraq “SI”]; twelve volunteers from each area. Seven primers (OP-A3, OP-A9, OP-B3, OP-C3, OP-D1, OP-C15 and OP-K2) were used in RAPD-PCR. Seven primers (14A, 44B, HB-9, HB-10, HB-11, HB-12, and HB-13) were used in ISSR-PCR. Results: Similarity coefficients and phylogenetic trees revealed the genetic distance and relationship of the studied groups as follows: the highest genetic overlap “similarity” was between SE and both NI and NE, respectively. The biggest genetic distance (variation) was between SI and both “NI and NE”. Conclusion: The study concluded that: (1) RAPD-PCR method was more valuable in detecting genetic polymorphism as compared to ISSR-PCR method, (2) Combined analysis using both RAPD and ISSR-PCR methods gave a clear indication of genetic variations than either RAPD or ISSR-PCR techniques