Antarctic marine biological variability modulates climate systems via the biological pump. However, the knowledge of biological response in the Southern Ocean to climate variability still has been lack of understanding owing to limited ocean color data in the high latitude region. We investigated the surface chlorophyll concentration responses to the Southern annular mode (SAM) in the marginal sea of the Southern ocean using satellite observation and reanalysis data focusing on the austral summer. The positive phase of SAM is associated with enhanced and poleward-shifted westerly winds, leading to physical and biogeochemical responses over the Southern ocean. Our result indicates that chlorophyll has strong zonally asymmetric responses to SAM owing to different limiting factors of phytoplankton growth per region. For the positive SAM phase, chlorophyll tends to increase in the western Amundsen–Ross Sea but decreases in the D’Urville Sea. It is suggested that the distinct limiting factors are associated with the seasonal variability of sea ice and upwelling per region.