The aim of this study was to apply RAPD technique to analyse the genetic relationship of two agamid lizard species, Leiolepis guentherpetersi and Leiolepis reevesii, collected from Thuy Phu commune, Huong Thuy town (16020’N, 107045’E) and Thuan An township, Phu Vang district (16030’N, 107040’E), belong to Thua Thien Hue province in Vietnam, respectively. The two single primes (428, and CRL5) and one pair-wise combinations of primers (101+268) used in PCR-RAPD analysis. The amplified PCR products were detected on a 1.5% agarose gel and subjected to further analysis to establish the band profiles and genetic relationships using the Quantity One software, the POPGENE software and the NTSYS-pc software. The percentages of polymorphic loci observed in the two populations were 28.26% (L.... guentherpetersi), and 15.56% (L. reevesii). The higher genetic diversity was found within the L. guentherpetersi population (0.0756), and lower genetic diversity was found for the L. reevesii (0.0566). The Shannon index ranged from 0.0944 (L. reevesii) to 0.1207 (L. guentherpetersi). The values of genetic identity and genetic distance between populations were 0.8523 and 0.1598, respectively. Phylogenetic analysis by RAPD showed two distinct but related clusters between the two populations. The similarity index value within the individuals of L. guentherpetersi obtained was 0.7755-1.0 while in L. reevesii individual’s ranges from 0.8571-1.0.