Amblypygi is a small order of arachnids with features similar to spiders. In Colombia, this order has been subject to low attention, the main investigations are focused towards a taxonomic level. Recently, the geometric morphometrics has proven to be an useful tool for determining shape differences in scorpions and spiders. Due to this, we used geometric morphometrics to determine intraspecific variation in three Colombian populations of Phrynus barbadensis. We digitalized 16 anatomical points over the carapace and 15 in patella by combining landmarks and sliding semilandmarks; the coordinates were aligned by generalized Procrustes analysis. Canonical Variates Analysis was implemented with proportions of re-classified groups and MANOVA. We found significant differences of carapace conformation between populations; all specimens were 80% correctly classified. Statistical analyses of variance (ANOVA) found significant differences in carapace and patella isometric size among populations; the main carapace differences occur in anterior, posterior and right margins. The observed variation could be associated with the environmental differences between localities