Based on the study of biodiversity features of forested areas, the irreplaceability values of conservation planning units can be calculated using the Systematic Conservation Planning (SCP) approach and C-Plan conservation planning software (C-plan). This approach selects representative endangered species as indicator species and their spatial distributions are then estimated using C-Plan. To analyze biodiversity hotspots in northeast China we used the planning function of C-Plan. According to existing conservation areas and the priority ratings of the area under study, a GAP analysis of biodiversity was performed. Depending on the irreplaceability value of each conservation planning unit, we divided areas into three levels of conservation priority, mandatory reservd areas (MR), negotiated Reserved areas (NR) and partially reserved areas (PR). The result shows that areas for MR priority, most of which lie in the core areas of Changbai Mountain and the virgin forests of the northern Great Khingan Mountains, accounts for 8.17% of the entire area under study; the NR areas, which mainly lie in the southeast of Great Khingan Mountains and the Songnen Plain wetland, accounts for 7.51%; and Partially reserved areas account for 9%. Results of GAP analysis show there are some evident protection gaps between priority planning areas and existing national nature reserves in northeastern China. Those are Changbai mountain area, north Great Khingan Mountains, the transitional area between western grassland and north Great Khingan Mountains area. In addition we studied the contribution existing nature reserves make to achieve the target of protection in different periods by using C-Plan, the results of which show the contribution value of the existing conservation areas to be 17.5% by the year 2000. By comparing contribution values of existing and planned nature reserves, we can decide the level of protection, guide the systematic planning of conservation areas, and support further development and strategies for conservation accordingly. Our research created a new approach to SCP for planning units, using natural polygons, such as vegetation types and landforms, instead of the traditional method using symmetrical shapes vastly improving the accuracy of the distribution range of species.