The stable isotopes ratios ($delta^{13}C;and;delta^{15}N$) of two coexisting species of zooplankton (Daphnia longispina and Acanthodiaptomus pacificus) and POM were determined in two alpine lakes in Japan. The difference of $delta^{13}C$ between A. pacificus and D. longispina was 4.1$pm$0.9‰ in Lake Shirakoma, which was larger than in Lake Panke. Whereas the difference of $delta^{15}N$ between A. pacificus and D. longispina (2.6$pm$0.8‰) was larger in Lake Panke than in Lake Shirakoma. $delta^{13}C$ of POM (-26.6$pm$1.2‰) in Lake Shirakoma was different from those of zooplankton; it was heavier than those of D. longispina and A. pacificus by 3.7$pm$1.6‰ and 7.8$pm$1.0‰, respectively. Whereas $delta^{15}N$ of POM (2.0$pm$0.8‰) was similar with those of both A. pacificus and D. longispina. This implies that the two lakes may have different trophic structure and food sources for zooplankton, and each species are grazing on selectively different components of POM. The temporal variation of $delta^{13}C$ for each zooplankton species was associated with lipid contents of zooplankton in both lakes. The results showed that stable isotope composition of zooplankton can be an useful information for understanding energy pathways and trophic structures in lakes.