Andean topography promoted lineage diversification in South America. However, there is a lack of evidence about its effect in arthropod divergence, especially in arachnids. In this study, the genetic connectivity among populations of the aquatic spider Ancylometes bogotensis (n=42) was tested using mitochondrial and nuclear DNA. A bogotensis was monophyletic and nested inside the Ctenidae family. This species was splitted in two divergent and structurated clades separated by the eastern cordillera of the Colombian Andes without gene flow. Divergence time for these clades were ~2.76Ma, matching the geological uplift of this cordillera. This study constitutes one of the few cases, where divergence caused by vicariance shaped the genetic diversity in an arthropod lineage.