A quarter of all lagomorph species worldwide are threatened with extinction. Captive breeding programs, such as that developed for the Columbia Basin (CB) pygmy rabbit (Brachylagus idahoensis), sometimes are implemented as emergency conservation measures to restore small, genetically distinct populations. However, small source populations also may have low genetic diversity, which may influence attributes related to fitness, including growth, survival, and reproduction. We used mixed-effects regression models to explore the influence of genetic pedigree (% CB) on pairing success, growth, and survival during the 10-year captive breeding program at Washington State University, which included controlled pairings and outbreeding with pygmy rabbits from Idaho. Pairing success, juvenile growth, and juvenile survival declined with increasing CB pedigree of 1 or both parents, suggesting inbreeding depression among the small number of related founders. Demographic variables such as age, sex, and previous pregnancies, and environmental variables such as month and temperature at birth also were associated with production of pygmy rabbits. Our study illustrates the difficulty of retaining a unique genome of a small source population while simultaneously producing enough rabbits for restoration into natural habitat as part of endangered species recovery programs.