Antarctica represents a unique natural laboratory for studying cold-adaptation, and the Southern Ocean offers a large source of ecosystems useful for exploring speciation and evolution in the absence of gene flow from outside biota. The Southern Ocean began to cool approximately 40 million years ago (mya), reaching the current temperature range of +2 °C to −1.8 °C approximately 25 mya (Clark et al. 2004). Therefore, Antarctic organisms live in extreme but stable conditions, i.e. very low mean temperature but very low variance. In this context, unicellular eukaryotes such as ciliates, found throughout the planet’s waters, with a phylogenetic position at an equal distance from plants and animals, offer a unique perspective on basic biological processes. The degree of structural and functional complexity of ciliates is comparable to that of human and other metazoan cells. They are comprised of a single cell but also organisms directly exposed to environmental changes. Ciliates are useful model organisms, as also demonstrated by two Nobel prizes awarded for work on ciliated protozoa: 1- the discovery of catalytic RNA in 1989 and 2- the discovery of how chromosomes are protected by telomeres and telomerase in 2009. The main research organism is Euplotes focardii, a strictly psychrophlic ciliate endemic of the Antarctic coastal seawater (Pucciarelli et al., 2009).