In comparison to organisms parasitising vertebrates, parasites of arthropods are direly understudied despite their abundance, importance, and potential usefulness. Due to their close relationship and coevolution with the host, parasites can be used as tools allowing the inference of information on host life history, ecology, and past events the host species has experienced. Even though parasites comprise a diverse assemblage of taxa, it is possible to identify convergent patterns in their genetic population structure. Predictions of congruent population genetic co-structuring between hosts and parasites can be thus based on a few traits such as host specificity, life cycle complexity or parasite and/or host dispersal. The parasite may even provide better resolution of population structure than the host itself, serving as a proxy that can be used to direct conservation projects of both the host and parasite. Our review provides an overview of known cases of host-parasite population co-structuring in arthropods, identifies their common patterns, and discusses practical applications of these findings.