The West Antarctic Peninsula (WAP) is associated with large phytoplankton blooms that are dominated by large (<20 microns) diatoms however, nanoplankton (>20 microns) are also an important component in the phytoplankton community. The dominant nanoflagellate in the WAP has been suggested to be cryptomonad algae. Using a twenty-year time series collected by the Palmer Long Term Ecological Research (Pal LTER) program, we assessed long-term patterns and stability in the coastal phytoplankton communities in the WAP. There was significant interannual variability in the integrated water column chlorophyll a (chl-a) concentrations, which varied by a factor of 5 over the 20-year time series. Within the time series the dominant phytoplankton taxa were diatoms, with the second most abundant phytoplankton taxa present being cryptophyes. While diatoms were observed over the full range of observed salinities (34.5 to 32) as well as over the full range of in situ temperatures (-1.5 to 2.5° C), the cryptophyte populations were observed in lower salinity (33.75 to 32.5) and colder water (-1 to 1° C) for the local time series at Palmer Station. This pattern was not observed for the ship spatial time series data, which might reflect the species diversity in the cryptophyte species between northern and southern waters of the WAP. Regardless, diatoms and cryptophytes were inversely related to each other across the entire WAP. Years when environmental factors favor water column stability, there are anomalously large summer diatom blooms. Consistent with modeling studies this suggests a potential shift to multivorous food web, which has significant ecological and biogeochemical implications, such as decreased efficiency of atmospheric carbon sequesteration.