A simple technique has been developed to probe the occurrence of cryptic genetic diversity in populations of laboratory-maintained phytoplankton cultures. This agarose-based method allows the investigator to plate a broad range of fragile algae, including representatives of the Raphidophyceae, Synurophyceae, Prymnesiophyceae, and Dinophyceae. Heterosigma akashiwo (Hada) Hada ex Y. Hara et Chihara was selected as a model system for our genetic diversity study. Further optimization of the plating technique for this alga demonstrated that colony formation was independent of the physiological state of the parent culture and yet dependent on incident light intensity. The density at which cells were plated affected colony formation and the rate of growth, with intermediate densities (∼103 cells per plate) performing best. High-metal stress was used as the selective screen for assessing genetic variability within a single H. akashiwo culture. To this end, “clonal” lines (quotation marks used to indicate that within-clone diversity was expected) were generated from individual plated colonies, and their tolerance was measured by plating on selective medium. Results of these experiments suggest the following: (i) “clonal” lines generated from a single H. akashiwo culture displayed a significant variation in stress tolerance; (ii) “clonal” lines chosen for their ability to grow on selective plates retained this tolerance in the absence of stress, indicating that the observed variation is heritable; and (iii) genetic variation is continually generated in growing cultures. Our results are consistent with a conceptual model, presented here, in which stress tolerance among the individuals in a culture has a genetic basis that varies over a continuous spectrum.