Species with undifferentiated sex chromosomes emerge as key organisms to understand the astonishing diversity of sex-determination systems. Whereas new genomic methods are widening opportunities to study these systems, the difficulty to separately characterize their X and Y homologous chromosomes poses limitations. Here we demonstrate that two simple F-statistics calculated from sex-linked genotypes, namely the genetic distance (F-st) between sexes and the inbreeding coefficient (F-is) in the heterogametic sex, can be used as reliable proxies to compare sex-chromosome differentiation between populations. We correlated these metrics using published microsatellite data from two frog species (Hyla arborea and Rana temporaria), and show that they intimately relate to the overall amount of X-Y differentiation in populations. However, the fits for individual loci appear highly variable, suggesting that a dense genetic coverage will be needed for inferring fine-scale patterns of differentiation along sex-chromosomes. The applications of these F-statistics, which implies little sampling requirement, significantly facilitate population analyses of sex-chromosomes.