This study aimed to evaluate the genetic and environmental factors affecting the survival of the pygmy hippopotamus (Choeropsis liberiensis) population kept in zoological gardens, including the estimation of the inbreeding level. Survival was examined at three time points: birth (0–1 days), 1 month (30 days) and 5 years of age. The data were obtained from the Zoological Information Management System, and covered observations on 1196 pygmy hippo, collected between 1873 and April 2016 and grouped into five geographical regions (Africa, Australasia, Europe, USA and Canada, and South America). The analyses were performed using LOGIT and PROBIT transformations of the binominal survival data. No statistically significant differences (P-value > 0.05) were observed between the results obtained from the two transformations. The survival of individuals was found to decrease with increased level of inbreeding, the most significant effect being on survival at birth. At all three survival time points the highest survival was observed among females. Additionally, the Australasia region showed the highest overall survival. We hypothesize that the environment, climate and similarity of local food to the native diet of pygmy hippo allows animals kept in zoological gardens in that region to perform better than in other regions. The results of this study indicated that it is necessary to exercise vigilance in reducing inbreeding as it negatively impacts survival. This can be achieved by continued efforts to maintain and improve genetic diversity through management of breeding and associated transfer of animals between zoological facilities to reduce relatedness in breeding pairs.