Population geneticists and phylogeographers are interested in understanding the processes that have shaped the present distribution and diversity of organisms and the genetic variation they contain. In this context, the analysis of spatial patterns of molecular variation within a species has a long- standing tradition. Recently, as a by-product of the rise of DNA barcoding efforts and technological progress, the availability of datasets on intraspecific variability has increased significantly. Re- searchers with many different backgrounds are therefore increasingly being faced with the need to carry out a meaningful analysis in the context of population genetics and phylogeography. A central limitation present in many studies today is that either a single or few mitochondrial gene fragments are being studied as a basis for reconstructing the genetic structure of species and inferring their evolutionary history, even though evidence is mounting that analyses based on a single marker in general, and on a single mitochondrial marker in particular, may be severely biased and may even lead to false conclusions. In this chapter, we emphasize that an independent class of markers should be chosen to com- plement a mitochondrial dataset. Accordingly, we outline a workflow based on several independent microsatellites in addition to mitochondrial DNA. This guideline builds upon earlier synopses and adds new perspectives afforded by novel laboratory and bioinformatic microsatellite screening pro- cedures. Finally, we summarize basic analytic concepts and common problems associated with their application and highlight the utility of different programs in a workflow towards a hypothesis-driven analysis of intraspecific variation. Where possible, we chose studies on crustaceans as examples.