For a long time, myriapods were considered as the sister group of the hexapods (insect and allies). However, analyses of molecular data have placed the Myriapoda either as sister groups of the Pancrustacea (Crustacea + Hexpoda), thereby supporting the monophyly of Mandibulata, or retrieve the Myriapoda as sistergroup of the Chelicerata. In addition, the relationships among the four myriapod classes (Pauropoda, Symphyla, Diplopoda, Chilopoda) is debated. To better resolve the phylogeny of myriapods, we obtained the transcriptomes (expressed sequence tags ESTs) from the centipedes Lithobius forficatus and Scolopendra subspinipes dehaani, and the millipedes Polyxenus lagurus and Polydesmus angustus by 454 next-generation sequencing.