The Western Ghats are globally recognized as a hotspot of rich, endemic and threatened biodiversity. Within this hotspot of biological diversity, there are islands of natural landscapes that can be termed as ‘hotspecks’. These hotspecks require careful prioritization and specific management strategies as they vary in objectives and ownership. Conserving hotspecks of biodiversity is of great relevance because creating new protected areas with wildlife corridors between them has become relatively impossible in the present context of intensive land-use change in this rapidly developing region. Management strategies, however, must be based on scientific assessment and using a set of prioritization criteria for selecting the most appropriate forms of management. The conservation action plan for the Western Ghats has become a controversial issue. In the present context of rapidly changing land-use patterns, economic development, forest fragmentation, isolation of habitats, linear intrusion, neo-urbanization and industrial growth are threats to the pristine nature of the ghats. Thus, there is an urgent need to identify, prioritize and manage the smaller fragments of biological importance within the larger ecologically sensitive landscape. A prioritization model for different types of hotspecks is essential so that it can be easily replicated by training frontline forest staff and implementing a strategy and action plans for the sites by using the Biological Diversity Act, 2002. Support of the local Biodiversity Management Committees and the State Biodiversity Board is essential for the conservation management of these biodiversity-rich sites.This study presents an innovative approach to prioritize areas (outside Forest Department jurisdiction) to assess the conservation value of hotspecks of diversity through a Rapid Biodiversity Assessment Technique. This can lead to a rational conservation strategy that conservation planners and practitioners can use.