Abstract The Hobby–Eberly Telescope Dark Energy Experiment (HETDEX) is an untargeted spectroscopic survey that aims to measure the expansion rate of the universe at z ∼ 2.4 to 1% precision for both H ( z ) and D A ( z ). HETDEX is in the process of mapping in excess of one million Ly α emitting (LAE) galaxies and a similar number of lower- z galaxies as a tracer of the large-scale structure. The success of the measurement is predicated on the post-observation separation of galaxies with Ly α emission from the lower- z interloping galaxies, primarily O ii , with low contamination and high recovery rates. The Emission Line eXplorer (ELiXer) is the principal classification tool for HETDEX, providing a tunable balance between contamination and completeness as dictated by science needs. By combining multiple selection criteria, ELiXer improves upon the 20 Å rest-frame equivalent width cut commonly used to distinguish LAEs from lower- z O ii emitting galaxies. Despite a spectral resolving power, R ∼ 800, that cannot resolve the O ii doublet, we demonstrate the ability to distinguish LAEs from foreground galaxies with 98.1% accuracy. We estimate a contamination rate of Ly α by O ii of 1.2% and a Ly α recovery rate of 99.1% using the default ELiXer configuration. These rates meet the HETDEX science requirements.