Although promiscuity is believed to be common among leporids, little is known about the mating system of free-ranging pygmy rabbits (Rrachylagus idahoensis). We used 16 polymorphic microsatellite markers and DNA extracted from tissue samples of 10 rabbits from 2 litters collected in east central Idaho to evaluate paternity. We incorporated maternal genotypes for better resolution and employed an exclusion approach to detect multiple paternity. Our results demonstrated multiple paternity at 6 of the 16 loci tested for each litter. These findings support the expectation that pygmy rabbits have a promiscuous mating system. It has been proposed that multiple paternity could lead to higher effective population sizes and help small populations maintain diversity. Given that pygmy rabbits persist in small and fragmented populations, a promiscuous mating system might be important for maintaining genetic diversity in free-ranging populations and could be advantageous for the captive breeding program.