This study decodes the compact 73.8 Mb genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. This study includes 8 cells of PacBio RSII data used to generate a PacBio-only assembly, Illumina short-read gDNA data used to polish the assembly, stage-specific RNA-seq data, two libraries of ATAC-seq data, two libraries of CAGE data, and a paired-end library for Trilobodrilus axi, a closely related species.