Abstract: The key scientific problems of ecosystem studies concerned with applications of carbon and nitrogen stable isotope tracers are systematically discussed.These stable isotope tracers may be usedto elucidate major energy path ways carbon sources and cycling in the ecosystems. The traditional approach of determining trophic levels is the dietary analysis, but gut content are ofter ground beyond recongnition by the gastric mill of animals. Contributions of energy sources to craysfish in the Jacks Fork River, Missouri OSA, determined using the stable isotope mixing model are similar to results of gut-content analysis uncorrected for different food types. Comparing with gut-analysis method, stable nitrogen analysis does not require estimates of assimilation efficiency, integrates resource use over loger time periods, and is less tedious, particularly when working with small organisms. Stable nitrogen isotope compositions are commonly used to represent the trophic structure of aquatic system from high arctic to tropical marine food webs. Adult lake trout, a top pelagic predator, from a series of lakes has been found that their δ 15 N values vary from 0.75% to 1.75%, a surprisingly wide range for one species. The length of the food chain can explain this variation, supporting the idea that δ 15 N is a food-web descriptor. Recent studies have shown that the use of δ 15 N analysis to characteristic trophic relationships can be useful for tracing biocontaminants in food webs. The PCBs biomagnification within a food web can be assessed quantitatively using the measurement of δ 15 N values and PCBs concnetration.Furthermore, the authors propose the application of the stable isotopes in brown tide, environmental pollution, establishing ecological dynamics model and molecular tracers.