The blunt-nosed leopard lizard (BNLL; Gambelia sila) is an endangered species endemic to the San Joaquin Desert of California. Understanding its diet is fundamental to the conservation of the species and its habitat. DNA metabarcoding leverages the power of high-throughput DNA sequencing to provide both higher taxonomic resolution and prey-detection capacity over traditional fecal diet analyses, particularly when diets are composed primarily of arthropods. We non-invasively collected fecal samples, genetically identified them to species, and then used DNA metabarcoding of the 16S mitochondrial DNA region to recover arthropod diet sequences. We then compared the sequences recovered from diet to a custom reference library of DNA sequences recovered from arthropods in the study area to facilitate a high taxonomic resolution of lizard diet. Our dataset resulted in >700 samples from BNLL and four other sympatric lizard species. From these, we identified >100 invertebrate diet items. This information will be used to identify the most abundant prey species for the BNLL and potential competitor species. The development of a custom reference library helped overcome the lack of existing sequence data for arthropods in a region of high endemism.