To learn more about the reproduction of animals in zoos and aquariums we are applying methods and analyses used to ascertain genetic diversity. Results of this work will not only benefit captive animals but can also be applied to conservation of species in the wild. To understand the range of genetic diversity within species requires obtaining and genotyping many samples for each species. We collected DNA samples from over 23,000 individuals representing 200 species of mammals. Since some animals are difficult to capture, and thus blood samples are not always available, we devised methods for efficient DNA analysis using noninvasive samples such as feces and hair. We stored these in a DNA database (the DNA Zoo), which also includes information on the geographical region in which the sample was collected and characteristics of the individual. We are going to develop The DNA Zoo so that it is able to link to cell bank. Using the DNA Zoo, we are identifying subspecies/populations/kinships by genotyping polymorphic markers such as microsatellites and mitochondrial DNA. Moreover, by analyzing genes on the sex chromosome, we can identify the sex of some bird species in which males and females are difficult to distinguish by observation alone. We are also surveying individual differences in functional genes related to personality traits (e.g. stress susceptibility) and reproduction. Introduction of the next-generation sequencer made marker isolation and meta-genome analysis easier, and widens the possibility of genome analysis of wild animals.