Intraspecific molecular and morphological variations among geographically isolated populations are useful for understanding the evolutionary processes, which is considered early stage of allopatric speciation. Also, the knowledge of the regional variation of scorpion venom composition is needed to improve antivenom therapeutic management. Androctonus crassicauda (Olivier, 1807) is the most common and medically important species in Arabia and the Middle East. Therefore, this study aimed to investigate the geographic morphological variation among A.crassicaudapopulations, regarding its geographical distribution in unexplored arid regions in Saudi Arabia. Samples were collected and examined morphologically under a dissecting microscope from different four eco-geographical regions. The results of ANOVA and multivariate statistical analyses provide strong evidence of geographical variation. The two populations from OTU3 and OUT4 showed the greatest degree of morphological difference from populations of OUT1 and OUT2. Each OTU3 and OTU4 populations showed significant speciation without overlapping in the two groups, while the remaining overlapped groups comprised two other populations. Several body variables influenced male separation, including carapace posterior width, metasoma 3rd length, and metasoma 2nd length. For females, telson length, metasoma 1st width, and sternite 7th width were highly influential variables. Such variation may suggest the existence of cryptic taxa within A. crassicauda populations in Saudi Arabia. Moreover, metasoma ratios can be used as good indicators in intraspecific variation studies of Scorpions.