Enviromental conditions, including such important climatic variables as temperature and precipitation, change with altitude; thus, elevation plays a significant role in determining population and community structure in a variety of organisms. Using single nucleotide polymorphisms (SNPs) and geometric morphometrics, nine populations of Culex theileri Theobald occurring in different ecological subregions at altitudes between 808–2,130 m in northeastern Turkey were compared. The wing size and shape data indicate that there are significant phenotypic differences among them, while Cx theileri populations are not genetically differentiated in the northeast part of Turkey. The size and shape variation analysis of wings showed that there is a positive correlation between wing (body) size/shape and altitude.