Our pigment analyses from a year‐long study in the coastal Beaufort Sea in the western Canadian Arctic showed the continuous prevalence of eukaryotic picoplankton in the green algal class Prasinophyceae. Microscopic analyses revealed that the most abundant photosynthetic cell types wereMicromonas‐like picoprasinophytes that persisted throughout winter darkness and then maintained steady exponential growth from late winter to early summer. AMicromonas(CCMP2099) isolated from an Arctic polynya (North Water Polynya between Ellesmere Island and Greenland), an ice‐free section, grew optimally at 6°C–8°C, with light saturation at or below 10 μmol photons·m−2·s−1at 0°C. The 18S rDNA analyses of this isolate and environmental DNA clone libraries from diverse sites across the Arctic Basin indicate that this single psychrophilicMicromonasecotype has a pan‐Arctic distribution. The 18S rDNA from two other picoprasinophyte genera was also found in our pan‐Arctic clone libraries:BathycoccusandMantoniella. The ArcticMicromonasdiffered from genotypes elsewhere in the World Ocean, implying that the Arctic Basin is a marine microbial province containing endemic species, consistent with the biogeography of its macroorganisms. The prevalence of obligate low‐temperature, shade‐adapted species in the phytoplankton indicates that the lower food web of the Arctic Ocean is vulnerable to ongoing climate change in the region.