The Arthropoda mitochondrial genome has been found to be relatively conserved in both, number and gene order. However, due to the sequencing of hundreds of mitochondrial genomes from different taxonomic groups of arthropods, it has been observed that certain clades have a typical numerical and organizational gene pattern. Although several studies have attempted to explain the evolutionary relationships among the four major arthropod lineages, the high variation in rearrangements between and within lineages remains controversial. The aim of this work was to compare the rate of mitochondrial gene rearrangements at inter and intra taxonomical level in arthropod, and to postulate the most parsimonious ancestral orders that represent the four major arthropod lineages. For this purpose, we performed a comparative genomic analysis of the arthropoda mitochondrial genome available in the NCBI database. Using a combination of bioinformatics methods to carefully examine the mitochondrial gene rearrangements in 464 arthropoda species represented in three Subphylum Chelicerata, Myriapoda and Crustacea (except for hexapods, previously analyzed). We determined that there is a great variation in the rate of rearrangement by gene and by taxonomic order. A higher rate of genetic rearrangement is observed in Crustacea and Chelicerata; compared to Myriapod. Likewise, within each subphylum, we identified that ancestral taxonomic orders tend to be more conserved than derived orders. From these data, we identify hot regions in the mitochondrial genome within each Subphylum, and postulate the most likely ancestral gene order in each Subphylum and taxonomic order. Our work provides new evidence on the evolutionary dynamics differentiate between different taxonomic groups of arthropods as well as their possible evolutionary mechanisms.