Antarctic coastal polynyas are biological hotspots in the Southern Ocean that support the abundance of high-trophic-level predators and are important for carbon cycling in the high-latitude oceans. In this study, we examined the interannual variation of summertime phytoplankton biomass in the Marguerite Bay polynya (MBP) in the western Antarctic peninsula area, and linked such variability to the Southern Annular Mode (SAM) that dominated the southern hemisphere extratropical climate variability. Combining satellite data, atmosphere reanalysis products and numerical simulations, we found that the interannual variation of summer chlorophyll-a concentration (Chl-a) in the MBP is significantly and negatively correlated with the spring SAM index, and weakly correlated with the summer SAM index. The negative relation between summer Chl-a and spring SAM is due to weaker spring vertical mixing under a more positive SAM condition, which would inhibit the supply of iron from deep layers into the surface euphotic layer. The negative relation between spring mixing and spring SAM results from greater precipitation rate over the MBP region in positive SAM phase, which leads to lower salinity in the ocean surface layer. The weak and negative correlation between summer Chl-a and summer SAM is possibly associated with high cloudiness in positive SAM phase that reduces the sea surface light irradiance. The relations revealed above are important for us to project the change in biological biomass in the study area based on projected change in the climate mode.