The dataset includes two alignment files in nexus format and supplementary figures and tables for the published paper. Title: Revisiting the phylogeny of Microsporidia Journal: International Journal for Parasitology https://doi.org/10.1016/j.ijpara.2021.02.005 1) An alignment of concatenated sequences (SSU rRNA + LSU rRNA) for the phylogeny of canonical Microsporidia 2) An alignment of SSU rRNA sequences for the phylogeny of Opisthosporidia. 3) Supplementary figures; all the full Bayesian and ML trees generated from the study 4) Supplementary tables; The lists of rRNA sequences used to infer the phylogenetic trees of canonical Microsporidia and Opisthosporidia