Molecular phylogenetics, interspecific comparisons, and assisted reproductive techniques are recent approaches to understanding and facilitating conservation of endangered species. This paper reviews the contribution of these approaches to a small but well-studied group of mammals, deer, many of which are endangered in the wild. Conservation efforts require a comprehensive understanding of the biology and history of these animals. The value of assisted reproductive technologies for conservation of deer has received increased awareness especially for captive populations. Such breeding programmes are designed to assist propagation of threatened species and to maximize genetic diversity within populations through the movement of genetic material across the globe, but will only be successful if we understand the genetic and reproductive potential of various lineages. Here we discuss the phylogenetic status of deer, the distinctiveness and evolution of their reproductive patterns, and current approaches for improving the success of controlled breeding programmes for the conservation of endangered lineages. Only by combining both theoretical and practical approaches to conservation efforts can we hope to salvage the remaining organismal diversity of our planet.