This study attempts to elucidate the position of chaetognaths, an enigmatic marine group using multigene phylogeny derived from transcriptome sequencing. Its main conclusion is that they group in Gnathifera together with rotifers. Our trees also suggest alternative relationships within spiralians with a new clade uniting annelid, platyhelminthes and nemerteans ('vermizoa'). This dataset contains alignments and raw output files from phylogenetic reconstruction generated in this study. 'alis.tgz' contains the raw individual alignments for each gene family. 'alis_filtered.tgz' contains the alignments after filtering with HMMClean and BMGE that were used in concatenation. 'cat-gtr-dh6.tgz' contains the bayesian sample (tree files and trace files with parameters) for the analysis conduced on the Dayhoff6 recoded dataset. 'cat-gtr.tgz' contains the bayesian sample for the analysis conduced on the non-recoded reduced dataset. 'Concat-alis.tgz' contains the alignments used for phylogenetic analyses. 'IQTree-C20.tgz' contains the run files for the IQTREE analyses of reduced dataset using C20 model. 'IQTree-LG4X.tgz' contains the run files for the IQTREE analyses if the whole matrix using LG4X model. 'Results_phylogenetic_analyses.pdf' contains all the consensus generated for this study