The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) is a unique freshwater subspecies of Neophocaena asiaeorientalis, which is endemic to the Yangtze River of China and is now critically endangered. Because its natural habitat is not expected to improve in near future, ex situ conservation was considered as the most important strategy to prevent it from distinction. However, in theory, without effective human intervention, inbreeding is unavoidable for any ex situ conserved small population. To evaluate the inbreeding level of the ex situ conserved Yangtze finless porpoise population living in Tian-e-Zhou National Natural Reserve, and to provide useful reference information for its population genetic management, 21 polymorphic microsatellite loci were utilized in this study to conduct parentage identification and to analyze relatedness among individuals in this population. As a result, three whole families with certain parents and offspring, together with 1 mother-offspring and 1 father-offspring pair have been detected. Yet, it is impossible to evaluate the inbreeding level of this ex situ conserved population according to so few parentages information. Nevertheless, relatedness analysis showed that the average relatedness index (r) of this population was 0.1182, and of the candidate parent pairs it was 0.1152. Both of them were significantly higher than those of the wild population living in the Poyang Lake. Additionally, in this ex situ conserved population, 26.14% of individual pairs have some relatedness (r > 0.2), which was 6 times higher than that of the wild population. Besides, inbreeding coefficient (Fis) of this population was 0.046. Results from both relatedness analysis and population inbreeding coefficient suggested that this ex situ conserved population is in high risk of inbreeding or has already been suffering from inbreeding. To prevent this ex situ conserved population from inbreeding or at least to mitigate the inbreeding level, on one hand, we recommend removing the adult female F34 and male M45 from this population because they had so many possible relatives. On the other hand, we recommend reintroducing two fertile porpoises (with an optimal sex ration of 1:1) every generation (about 5 years) from wild population or other ex situ conserved populations. Besides, to facilitate future population genetic management, constructing an accurate genetic studbook was proposed for this ex situ conserved population.