To study effects of variations in climate-marine environment in the Arctic Ocean on ecology, based on the actual and reestablished data by biomarkers of algae in sediment in 1997, 1999, 2003, 2008, and 2010, the interannual and spatial variations of phytoplankton, zooplankton and chlorophyll a concentration in the Chukchi Sea and the Bering Sea as well as their relations to El Nino-Southern Oscillation (ENSO) and Arctic Oscillation(AO) were analyzed. The results show that there were spatial and temporal anomalies in the phytoplankton community structure reestablished by biomarkers of algae in the Chukchi Sea and the Bering Sea in 1999 and 2010. The total content of biomarkers (brassicasterol, dinosterol, alkenones and chlesterol) in sediment collected in 2010 was far lower than that in 1999, but brassicasterol was dominant in the two years, that is, diatom was dominant, which was consistent with the actual structure and distribution of phytoplankton community in 1999 and 2010; there were great changes in the dominant species of plankton in the two seas in 1999 and 2010, which could be regarded as the ecological response of the North Pole under the background of global warming. Chlorophyll a concentration in the water of the Bering Sea was 0.720 Mg/dm3 at 0 m and 0.765 ng/dm3 at 10 m in 1997 and 0.723 ng/dm3 at 0 m and 0.731 nQ/dm3 at 10 m in 2003, and the concentration was very close to each other, which was affected by Nifio and the negative phase of AO. It was 0.395 nQ/dm3 at 0 m in 1999 and 0.399 uQ/dm3 at 0 m and 0.357 ng/dm3 at 10 m in 2008, which was influenced by La Nina and the positive phase of AO. The phases and intensity of AO and ENSO had various effects on the quantity and dominant species of phytoplankton and zooplankton in the Chukchi Sea and the Bering Sea. During the period of AO with positive or negative phase and NiPio (in 1997 and 2003),their combination was favorable to the growth of phytoplankton and zooplankton,while the combination of negative phase of AO and La Nina (in 2010) had ad