Among protists, ciliates (Ciliophora, Alveolata) are the best candidates for investigation of their endosymbiotic community due to their culturability under laboratory conditions and their presence in a wide variety of environments including ultraoligotrophic niches. However, a lesser number of isolation techniques are reported to date to separate and cultivate the endosymbiont from various ciliate species under lab conditions. This present chapter specifically deals with the isolation of algal endosymbionts from freshwater or marine ciliates. The technique involves micromanipulation of the ciliate, rupturing the cell to release endosymbiotic algae followed by enrichment of endosymbiont on complex media.