In this study, we analyse the evolutionary dynamics and phylogenetic 
implications of gene order rearrangements in five newly sequenced mitochondrial 
(mt) genomes and four published mt genomes of isopod crustaceans. The sequence 
coverage is nearly complete for four of the five newly sequenced species, with 
only the control region and some tRNA genes missing, while in Janira maculosa 
only two thirds of the genome could be determined. Mitochondrial gene order in 
isopods seems to be more plastic than that in other crustacean lineages, making 
all nine known mt gene orders different. Especially the asellote Janira is 
characterized by many autapomorphies. The following inferred ancestral isopod mt 
gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, 
control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred gene 
translocation events leading to gene rearrangements as valuable characters in 
phylogenetic analyses. In this first study covering major isopod lineages, 
potential apomorphies were identified, e.g., a shared relative position of trnR 
in Valvifera. We also report one of the first findings of homoplasy in 
mitochondrial gene order, namely a shared relative position of trnV in unrelated 
isopod lineages. In addition to increased taxon sampling secondary structure, 
modification in tRNAs and GC-skew inversion may be potentially fruitful subjects 
for future mt genome studies in a phylogenetic context.