European inland surface waters are home to a rich diversity of native amphipod crustaceans, many of which face threats from invasive Ponto-Caspian counterparts. In this study, we analyse mitochondrial genomes to deduce phylogenetic relationships and compare gene order and nucleotide composition between representative native European and invasive Ponto-Caspian taxa across five families, ten genera and 20 species (with 13 newly sequenced herein). We observe various gene rearrangement patterns in the phylogenetically diverse native species pool.Pallaseopsis quadrispinosaandSynurella ambulansexhibit notable deviations from the typical organisation, featuring extensive translocations of tRNAs and the nad1 gene, as well as a tRNA-F polarity switch in the latter. The monophyletic invasive Ponto-Caspian gammarids display a conserved gene order, primarily differing from native species by a tRNA-E and tRNA-R translocation, which reinforces previous findings. However,Chaetogammarus warpachowskyishows extensive rearrangement with translocations of six tRNAs. The invasive corophiid,Chelicorophium curvispinum, maintains a highly conserved gene order despite its distant phylogenetic position. We also discover that native species have a significantly higher GC and lower AT content compared to invasive species. The mitogenomic differences observed between native and invasive amphipods warrant further investigation and could provide insights into the mechanisms underlying invasion success.