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Results: Most of larval water types were man-made artificial sites, and belonged to 10 water container or habitat categories for different uses (average productivity: 83.9±103.6 larva/site, 5.4±7.4 pupa/site). SNPs and NJ analyses of single and concatenated marker sequences identified different molecular haplotypes unique to Saudi Arabian Ae. aegypti populations and numerous haplotypes shared with Ae. aegypti from other zoogeographic regions. Microsatellite loci showed that Ae. aegypti from Saudi Arabia is most closely-related to Asian populations, although they are genetically distinct. These results indicate the presence of considerable genetic variation among the studied Ae. aegypti populations from Saudi Arabia and other world zoogeographic regions.Conclusion: This is the first report on Ae. aegypti phylogenetics from the Arabian Peninsula, the most eastern part of the Afrotropical zone, and bordering the Palaearctic and Oriental zones. These results are important for better understanding of dengue transmission and implementation of control programmes at both the national and global levels.