DNA barcoding provides species-level identification when traditional techniques are challenging or inadequate.  Two rare species of stonefly, Capnia lineata and C. zukeli, appear to be nearly endemic to a single county in Idaho (Latah). Both are species of conservation concern at the state level and have been petitioned for listing under the ESA.  However, few details of range, habitat requirements or life history are available because adults are required for morphological identification but emerge only during a brief period in spring. We are developing targeted DNA assays to determine the distribution and habitat requirements of both species and the approach can be applied to other rare or endemic species of concern.