In mosquitoes of medical importance, wing shape and size can vary with altitude, an aspect that can influence dispersion and, consequently, their vector capacity. Using geometric morphometry analysis, Aedes aegypti wing size and shape variation of males and females was studied in four altitudes in the second-smallest department in Colombia: 1,200 m (Tebaida), 1,400 m (Armenia), 1,500 m (Calarcá), and 1,700 m (Filandia). Wing shape in males (P < 0.001) and females (P < 0.001) was significantly different through the altitudinal gradient; in turn, wing size in males followed the altitudinal gradient males (R2 = 0.04946, P = 0.0002), females (R2 = 0.0011, P = 0.46). Wing allometry for males (P < 0.001) and females (P < 0.001) was significant. Likewise, the shape and size of the wings of males (P < 0.001) and females (P < 0.001) had significant fluctuating asymmetry. It is concluded that, in a small scale with an altitudinal variation of 500 meters, it is detected that the size and shape of the wings varied in A. aegypti, main vector the agents that cause dengue, chikungunya, and Zika. The fluctuating asymmetry is present in the individuals studied and could be associated with environmental effects caused by vector control campaigns present in some sampling locations.