Pycnogonida, or sea spiders, is a speciose clade with over 1300 described species that is especially diverse in the Southern Ocean. Evolutionary patterns within sea spiders remain unresolved between and within the eleven putative, extant families due to shared morphological traits and highly reduced forms. A consensus phylogeny of recognized families is still debated, and previous work based on various methodologies has produced contrasting hypotheses of relationships. To better understand phylogenetic relationships between major clades of sea spiders, we constructed a dataset of mitochondrial genome data from representatives of all eleven currently recognized families. Herein, we find that the order of mitochondrial protein-coding genes is consistent between all sampled sea spiders, even though arrangement of tRNA genes, as well as placement and length of the control region, varies. The presence of large non-coding introns present in multiple families indicates that pycnogonid mitochondrial genomes have a fast evolutionary rate. Our results suggest a new, familial-level phylogeny within Pycnogonida, with a monophyletic clade containing Callipallenidae and Nymphonidae placed as the sister clade to all other recognized families.