California ground squirrels (Otospermophilus beecheyi; CAGS) and endangered San Joaquin kit foxes (Vulpes macrotis mutica; SJKF) frequently occur sympatrically. CAGS control strategies include lethal measures administered within CAGS burrows, which could harm or kill a SJKF if mistakenly applied to an occupied SJKF den. To identify attributes to distinguish between SJKF dens and CAGS burrows, we assessed dimensions, penetration depths, ejecta patterns, and the presence of various types of sign at 65 known SJKF dens and 80 CAGS burrows. Mean entrance height, width, and circumference all were significantly larger for SJKF dens. However, the ranges of values for all dimensions for the CAGS burrows encompassed the ranges for the SJKF dens. Penetration depth analyses revealed some general trends, but few absolute criteria to distinguish between the two. Dirt berms, scat, prey remains, and trash were observed at both SJKF dens and CAGS burrows. None of the attributes we assessed provided unequivocal criteria for distinguishing between SJKF dens and CAGS burrows. Also, SJKF occasionally usurp CAGS burrows and CAGS occasionally move into SJKF dens. Therefore, administering lethal control measures within burrows should be avoided as it presents a risk to SJKF and many other species that may use CAGS burrows.