AbstractRecent advances in molecular ecology opened a new chapter in conservation biology study. Disadvantages such as the long2duration of field studies , limited resolution and difficulties in the cont rol of experimental conditions in t raditionalecology research are seen to be overcome by molecular ecology methods. Molecular markers (RFL P , VNTR , RAPD , mitochondrial DNA , etc. ) provide efficient tools for the analyses of phylogeographic patterns , metapopulation dynamics , gene flow , population bottleneck effect s and individual relatedness. All of these are very important for biodiversity conservation and restoration of declining species. Species or race specific molecular markers could help to clarify ambiguity in morphological classification , phylogenetic relationships and possible hybridization among closely related taxa. This would be useful for defining the priority in species protection and the selection of protected areas. Recently , genomic regions encoding the major histocompatibility complex (MHC) were used to evaluate various specific questions such as population susceptibility to diseases and appear promising for future analysis. The continuing development of molecular technology will further enhance conservation ecology study. Studies based on multiple molecular marker systems when combined with ecological , demographic , behavioral and physiological data collected in the field , would provide a more definitive assessment of various conservation issues.