Xanthoid crabs, including mud and stone crabs, are integral to coastal ecosystems, particularly in habitats like oyster reefs, salt marshes, and coral reefs. These species contribute to ecosystem functioning and serve as a food source for economically and ecologically important marine organisms. However, their evolutionary relationships remain poorly defined, largely due to limited genetic data based on a small set of molecular markers. Additionally, comprehensive mitochondrial genome data for these species is sparse. This research seeks to address these gaps by employing shallow whole genome sequencing (WGS) to produce complete mitochondrial genomes and sequences for nuclear repetitive regions. Utilizing DNA extractions from more than 120 species, representing nearly every major xanthoid lineage, we aim to conduct phylogenomic analyses and examine its implications for broader ecological and evolutionary studies.