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In the present study, we focused on three populations of Persian Horned Snake, Pseudocerastes persicus from Iran and examined them morphologically. Geometric morphometrics is an appropriate method to evaluate the scale positions and shape in different populations of a given species in snakes. We used this method to evaluate the geographic variation among three populations of Pseudocerastes persicus. Based on variance and multivariate analyses, all populations from Isfahan, Semnan and Markazi provinces don’t show variation in head scales. This result from morphological features confirmed the previous molecular study on these populations. We recommended examining further taxonomic characters of these populations as karyotype and allozyme features.