Stenonema, Stenacron, and Maccaffertium are three closely related genera of mayflies commonly found across North America. There are currently 22 described species in Maccaffertium, 7 described species in Stenacron, and 1 described species in Stenonema. Their primarily aquatic life history, and sensitivity to aquatic pollutant make these organisms ideal water quality indicators. However, there is little morphological variation within these genera leading to difficulties in identifications. The classifications of many of the species within these genera have been changed multiple times and still little is known about the relationships with in these genera. In an attempt to resolve the phylogenetic relationships of Stenonema, Stenacron, and Maccaffertium, two Mitochondrial genes (Cytochrome oxidase subunit 1 (cox1), and 16s ribosomal RNA (rrnl)) and two Nuclear genes (Wingless (Wg), and Histone H3) were sequenced from 60 individuals from the three genera, and ten individuals from three outgroup genera (Pseudiron, Epeorus, and Heptagenia). Maximum likelihood and Bayesian analysis were conducted on single-gene and concatenated multi-gene data sets, and species tree methods were utilized to resolve the phylogenetic relationships. Molecular analysis resolve Maccaffertium as paraphyletic, with Stenonema femoratum being resolved within Maccaffertium, as sister to M. mexicanum integrum. Stenacron in most cases was also resolved within Maccaffertium, as a close relative of M. lenati. In order to achieve monophyly, Stenonema needs to be expanded to include Maccaffertium and Stenacron, and four subgenera should be erected to name the well supported clades; Stenonema, Maccaffertium, Stenacron, and Lewisa.