We determined the complete mitochondrial (mt) genome sequences of two northern hemisphere freshwater crayfish species, Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae). These species have an identical gene order with typical metazoan mt genome compositions. However, their gene arrangement was very distinctive compared with the pan-crustacean ground pattern because of the presence of a long inverted block, which included 19 coding genes and a control region (CR). Because the CR was inverted, their nucleotide frequencies showed a reversed strand-specific bias compared with the other decapods. Based on a comparative analysis of mt genome arrangements between southern and northern hemisphere crayfish and their putative close marine relative (Homarus americanus, a true clawed lobster), we postulated that the ancestor of freshwater crayfish had a typical pan-crustacean mtDNA gene order, similar to its marine relatives. Based on this assumption, we traced the most parsimonious gene rearrangement scenario of the northern hemisphere crayfish. In a phylogenetic study on the infraordinal relationships in reptan decapods, the lineage Lineata [Thalassinidea (Brachyura, Anomura)] was well supported, while the infraorder positions of Achelata and Astacidea remained unidentified.