show Abstracthide AbstractThe intraspecific genetic structure and diversity within the Humboldt's flying squirrel (Glaucomys oregonensis) has not yet been characterized despite its elevation to full species in 2017. The San Bernardino flying squirrel (G. o. californicus) is thought to be the southernmost population of G. oregonensis and is restricted to the San Bernardino and San Jacinto Mountains in California, but recent surveys indicate they have been extirpated from the latter locality. We amplified and sequenced approximately 300 bp of the mitochondrial cytochrome-b gene and 11 nuclear microsatellites in a total of 147 samples (tissue, hair, and museum specimen) using the Illumina high-throughput sequencing platform to investigate the genetic structure and diversity within this species and subspecies.