Habitat use, diet, prey availability and foraging ecology of the endangered Hawaiian hoary bat (Lasiurus cinereus semotus, Vespertilionidae), was examined in the east Maui region inclusive of the Waihou Mitigation Area, Pu‘u Makua Restoration Area and the wind power facility operated by Auwahi Wind Energy, LLC. Research for the bat ecology study was provided by Auwahi Wind Energy, LLC, in order to fulfill requirements for mitigating bat fatalities under its approved incidental take permit. This study included the first genetic analysis of Hawaiian hoary bat guano items, and broadly confirms the major arthropod orders (Coleoptera, Lepidoptera, Diptera, Hemiptera, and Blattodea) found in previous microscopy-based studies of guano samples. This dataset describes the representative DNA sequences of operational taxonomic units (OTU) of prey items found in bat guano, derived with two different primers (Zeale, Epp).