Thriving in the freezing polar seas forces organisms, in particular the unicellular ones directly exposed to the extracellular environment, to adaptively modify the lipid composition of their cellular membranes in function of maintaining an appropriate degree of fluidity. To seek into these modifications, we carried out a comparative analysis of the membrane lipid composition in four marine species of the globally distributed ciliate, Euplotes. Two, E. focardii and E. nobilii, are polar species that differ ecologically and physiologically from one another. The former is endemic to the Antarctic coastal waters and strictly psychrophilic (it does not survive over 10 °C), while the latter is characterized by a bipolar distribution and a psychrotrophic (rather than psychrophilic) behavior (it reproduces up to 15 °C). The two other species, E. crassus and E. raikovi, are widespread in temperate seas and phylogenetically closely related, the former, to E. focardii and, the latter, to E. nobilii. With respect to their temperate-water relatives, E. focardii and E. nobilii appear to similarly rely on significantly increased concentrations of lipid molecules with higher unsaturation indices and a conical shape to maintain an appropriate degree of membrane fluidity and curvature. Nevertheless, they markedly differ from one another in the membrane lipid composition. In the E. focardii membranes, a single lysophosphatidylcholine molecular species accounts for 17.8% of total glycerophospholipids and only 118 structurally distinct lipid molecules are identified, of which 38 are phosphatidylcholines and eight are phosphatidylethanolamines. In the E. nobilii membranes, phosphatidylethanolamines represent 47.3% of total glycerophospholipids and 226 distinct lipid molecules are identified, of which 115 are phosphatidylcholines and 55 are phosphatidylethanolamines. These functionally significant differences in the lipid membrane composition between the two polar species likely reflect a more stringent cold-adaptation strategy evolved by E. focardii which is exposed to a constantly subzero temperature in relation to its Antarctic endemism, and a more flexible strategy adopted by E. nobilii to face more variable temperatures in relation to its bipolar distribution and trans-equatorial migration via the deep ocean currents.