Limited dispersal and cooperation are predicted to coevolve in cooperatively breeding systems. In Polistes paper wasps, mark-recapture studies and genetic analyses have shown that both cooperative and solitary nesting gynes can exhibit natal philopatry. Male dispersal has not been studied in Polistes, therefore the potential effects of sex-biased dispersal on population structure are unknown. In this study I used whole genome re-sequencing data from Polistes fuscatus wasps collected across the Eastern US to assess demographic history and population structure within a well-studied cooperatively breeding system. In order to deduce the influence of sex-specific dispersal patterns on overall population structure, I analyzed population structure using nuclear as well as mitochondrial genomes. While low pairwise Fst values indicated overall depressed levels of genetic differentiation, I found a consistent and significant pattern of spatial genetic clustering and isolation by distance in both the nuclear and mitochondrial genomes, supporting the hypothesis that limited female dispersal contributes towards population structure in P. fuscatus wasps.