The endangered African painted dog (Lycaon pictus) faces numerous threats in the wild. Ex situ conservation efforts are hampered by unpredictability in reproductive outcomes, leading to demographic instability and challenges for genetic management. Here, we describe a series of studies designed to contribute to the sustainability of conservation efforts for African painted dogs and other endangered species. First, we use a genotyping-by-sequencing approach to produce a population-level dataset of genome-wide SNP data for the African Painted Dog Species Survival Plan (SSP) population. We give a genomic description of the population based on these data, and provide a framework for efficient genotyping for possible future use in meta-population management strategies. Next, we monitor glucocorticoids and progestogens in 20 SSP packs over a 1-year period. We characterize female reproductive cyclicity in the population, identifying 4 females that are acyclic for unknown causes. We further investigate the relationship between rank and glucocorticoids in the cooperatively breeding species, and find that this relationship depends upon reproductive status. Third, we investigate the causes of poor reproductive outcomes, and find that pair relatedness, social structure, female age, prior litters, enclosure size, climate control, and fecal glucocorticoid metabolites are all related to reproductive outcomes. Last, we use the domestic dog model to investigate how different levels of inbreeding are linked to a trait of fitness relevance: average life expectancy. The combined results of these studies are used to develop management recommendations to improve outcomes for painted dog conservation, and a framework for using a similar approach for other species.