AbstractFarm animal genetic resources have been threatened over the past decades, therefore a scientific and efficient framework is critical to allocate limited funds to conserve maximal genetic diversity of farm animals. In this study, the marginal diversity method was exploited to set priorities for conservation of 18 Chinese pig breeds. Based on the analysis of their extinction probability, contribution rate, marginal diversity, and conservation potency, we evaluated the effectiveness of three models to gain the maximal expected diversity and optimal fund allocation. The additive model (model A) proved to be optimum for allocation of all the funds to 10 of the 18 Chinese pig breeds. The largest share of funds (16%) was allocated to the Hang pig, followed by the Ganzhongnan spotted pig/Wanan pig and Shengxian pig (which earned 14% each), the Yangxin pig and Leping pig (11% each), the Wuzhishan pig (10%), the Yushan black pig and Ganzhongnan spotted pig/Guanchao pig (9% each), and the Qingping pig, Wuyi pig and Jiaxing pig (2% each). The results indicate that the degree of endangerment, genetic diversity, economic importance and contribution of breeds to the species diversity should be taken into account when allocating conservation funds.