While natural populations of large predators decline, captive populations are increasingly being considered as potential reservoirs of genetic diversity because they may house genomic variants that are rare or extinct in the wild. However, the genome-wide effects of long-term captivity and the artificial selection of zoo breeding programs have not been extensively studied. Furthermore, captive programs have limited information on the initial genetic diversity of the individuals that contribute to the founding population, so pedigree-based analyses of inbreeding and diversity statistics may be uninformative to breeding programs. This lack of knowledge of the genetic diversity housed in captive populations inherently inhibits our predictions on the benefits and potential integration of captive populations into the wild. Here, we evaluate the accuracy of pedigree-based diversity analyses compared with those computed by low-coverage genome analyses from tiger populations in the US and India. We also investigate the genomic differences between captive and wild tigers as a first pass at how captivity affects the genomic landscape. Of the three populations kept under AZA management (Association of Zoos and Aquariums), the Amur tiger population is the largest, while the Sumatran, and Malayan populations are considerably smaller and come from smaller founding populations. The analyses from this study provide considerable evidence for using genetics as an additional management tool, in addition to a much needed evaluation of diversity of our captive tiger populations.