The oriental red spider mite, Eutetranychus orientalis (Klein) is a major pest of citrus in many countries including Saudi Arabia (SA). The morphological variations among the different populations of E. orientalis were reported. In the present study, phenotypic variations based on 40 different morphological characteristics were evaluated in 10 E. orientalis populations collected from different hosts and regions of SA. Further, ITS2-rDNA sequences were used to confirm the identity of these phenotypically varying populations. Phenotypic variations in all populations were found in the shape and length of dorsal setae, striation pattern between setae d1 and e1, and leg chaetotaxy. The rDNA sequence analysis of these morphologically varying populations resulted in 10 different ITS2 Saudi haplotypes. The phenotypic and genetic variations were more related to the host plants rather than their geographic distribution. The E. orientalis population collected from Phoenix dactylifera was phenotypically distinct and genetically divergent. The populations collected from citrus species were also more phenotypically and genetically related to each other than to populations collected from non-citrus host plants. The haplotypes recovered from Ziziphus sp., Morus sp., and Azadirecta indica from different regions were grouped in the same sub-clade. Further, the ITS2 haplotypes of Saudi E. orientalis recovered from Citrus reticulata from Riyadh and Al Ula were 100% identical to the ITS2 haplotypes recovered from Citrus sp. from Israel. It is concluded that phenotypic variations exist among different populations of E. orientalis inhabiting different host plants. This species should be identified carefully by considering phenotypic intraspecific variations.