Bio-diversity monitoring is undertaken by Chinese Academy Society, Northwest Soil and Water Conservation Institute, MWR, besides, Longdong University of Gansu Province, Soil and Water Conservation Research Institute of Qingyang City also participate in it. By one-year field survey, data collection and analysis, the project has been completed, and the consulting agencies have delivered Bio-diversity M & E Report. Based on analyzing and evaluating effects of control measures on bio-diversity in watershed, mainly the four selected pilot ones, and using data and achievements of related watershed as a reference, the report designs questionnaire that can be used in evaluation of effects on sub-watershed bio-diversity, and puts forward Biology (Species) Diversity Monitoring Index and Method, which can referred by Yellow River monitoring agencies and similar projects in the future, and which methods propose primary bio-diversity monitoring system, index and evaluation methods, and has laid a foundation for establishing primary bio-diversity M & E system in Loess Plateau.