The entire range of the critically endangered Amargosa vole (Microtus californicus scirpensis) consists of less than 20 km2 of riparian habitat in the Amargosa River drainage of the Mojave Desert in southern California. In September 2010, deformities on ears and chiggers on the ears and genitalia were detected, with some individuals so severely affected that they were missing ear pinnae altogether. Follow-up trapping was performed to document the presence of mites and mite-associated disease, and molecular characterization was performed on the mites. Of 151 Amargosa voles sampled from February to April of 2011, 60 (39.7%) voles had hard orange mites adhered to some part of their bodies, on ears of 46 (76.7%), on genitalia of 11 (18.3%), and near mammary tissue of 13 (21.7%) voles. Gross lesions were not detected on genitalia, but 47% of all individuals examined showed pinnal lesions and deformities, which included alopecia, swelling, marginal necrosis, and ulceration, as well as scarring, scabbing, and loss of pinna mass covering 25–100% of the pinnae. Biopsies revealed parakeratotic hyperkeratosis and acanthosis with diffuse neutrophilic exocytosis and dense necrotic granulocytes in the epidermis and superficial dermis associated with focal erosion and ulceration. In the underlying dermis, there were dense pleocellular inflammatory cell infiltrates composed primarily of necrotic granulocytes and multifocal hemorrhage. In some samples, mite mouthparts could be seen penetrating the superficial epidermis associated with focal necrosis, and mite fragments were found on the surface epidermis and within hair follicles. Microscopic examination of the mites documented that they were a larval trombiculid in the genus Neotrombicula with anatomical features that most closely resemble Neotrombicula microti, based on scutal shape, setation, and texture. PCR of 2 mite pools (each consisting of 3 mites from an individual animal) amplified 331 bp amplicons, which had 92–97% homology with the 18S rRNA gene of Leptotrombidium deliense, although coverage of Trombiculidae in GenBank is sparse. The severity and prevalence of lesions due to this chigger were atypical and distinct. Severe clinical trombiculiasis in this endangered species could negatively impact individual health and fitness.