Noninvasive genetic sampling is an essential tool for studying elusive and endangered species. However, the DNA from noninvasive genetic sampling tends to be low in quantity and quality, which leads to poor DNA amplification. Using fecal pellets of pygmy rabbits (Brachylagus idahoensis) collected in February, March, and November 2011, we tested a possible solution of increasing the amount of sample by combining multiple pellet groups during DNA extraction. One potential drawback of this approach is accidental mixing of samples from multiple species. This study evaluates the mitochondrial DNA (mtDNA) species identification success rate for pygmy rabbit (PY) fecal DNA when mixed with eastern cottontail (Sylvilagus floridanus; EC) fecal pellet DNA at lower frequencies (1PY:3EC and 2PY:6EC) and eastern cottontail or mountain cottontail (S. nuttalli) pellet samples at an equal frequency (4:4). We found that successful detection of pygmy rabbit DNA using a species-specific mtDNA polymerase chain reaction (PCR) test varies from 0% to 95% depending on the competing species and PCR protocol. From these results, we conclude that if samples are unintentionally mixed, the species with a greater number of pellets within the sample will be more likely to be detected. Also, if pellet piles are intentionally mixed to reduce sampling cost, the protocol should be optimized to maximize DNA amplification for the focal species; however, there will be reduced detection rates depending on the quality and quantity of the focal species DNA within the sample. © 2013 The Wildlife Society.