The emergence of comparative phylogeography requires tools that allow comparing quantitatively the genetic structures between species. Whereas numerous methods have been developed to compare trees inferred from two species, comparison methods involving population structures issued from Bayesian inferences or maximum likelihood criterion have been poorly investigated. Here, we present a method implemented in an r (CRAN) scripts collection, SIMIL, based on the mean absolute differences computed from structure 2 outputs. The scripts collection is illustrated by the computation of unweighted and weighted genetic-structure-similarity (GSS) indices in three alpine plants. Different weighting procedures — taking into account the level of overlap between the species sampling areas — are compared among the different species pairs and among the different numbers of gene pools considered in structure.