Capture-recapture is a powerful, if expensive and difficult, approach to estimate abundance. Noninvasive genetic sampling is a potential alternative, but methods vary among taxa with little research on its use in rodents. We addressed a series of questions to develop a noninvasive genetic sampling approach for the endangered giant kangaroo rat (Dipodomys ingens). Over 2 years, we used 2 sampling grids, first live trapping and then collecting and genotyping fecal pellets. We found that fecal pellets were successfully genotyped up to 9 days (93%) after exposure, but that rate precipitously fell soon after. Although giant kangaroo rats are territorial, multiple individuals deposited fecal pellets at the same sampling locations; however, single pellets contained sufficient DNA to recover genotypes and to identify individuals, so contamination was not a problem. Per occasion capture probabilities were lower in noninvasive genetic sampling (p = 0.26, SE = 0.01) than from live trapping (p = 0.42, SE = 0.06). Population estimates were similar using noninvasive genetic sampling, although they were quite a bit higher (Ntrap = 36, Nfecal = 64) on one grid. Noninvasive genetic sampling should be tested in additional taxa and systems to provide more generalizable recommendations.