Current hypotheses of the relationships of major mayfly lineages remain controversial due to low nodal support of previous phylogenetic studies dealing with both morphological and molecular data. Contradictions in these studies have led to classification systems that do not accurately depict the evolutionary history of Ephemeroptera. The present study seeks to clarify these disputed relationships by leveraging targeted capture sequencing along with a novel hybrid enrichment pipeline to generate abundant amounts of data, bolstering the confidence in the topology produced herein. Nearly 500 highly conserved exonic regions of the genomes of approximately 150 distinct taxa were targeted for amplification and sequencing using a custom probe set (Ogden et al., 2019). The next generation sequence reads were parsed in a custom pipeline and the fully assembled reads were appended in a single supermatrix for phylogenetic analyses using both 1st and 2nd nucleotide positions and amino acid sequences. This is the most robust analysis of Mayfly phylogeny to date, and indicates that current mayfly taxonomy necessitates revision.