BackgroundChrysochromulina (Haptophyta) species are recognized as seminal contributors to marine and freshwater ecosystem function. Historically, scale vestiture is used to augment taxonomic identification of these algae, and a large literature exists concerning the morphology of many scale-covered representatives. Scale-less freshwater isolates present a new challenge. Details concerning the microanatomy of naked cells remain essentially unreported. Insight into morphological similarities/differences between scaled and naked cells provides information on the evolution of the taxon, especially as discussions defining cryptic species complexes become more germane. Using light, scanning, and transmission microscopy, we present an analysis of the cellular structure for three Chrysochromulina freshwater isolates. ResultsChrysochromulina tobinii Cattolico, Chrysochromulina parva Lackey and ChrysochromulinaAND cells are approximately 5 μm wide, saddle-shaped to globose, and devoid of scales. A lipid body is nestled close to each of two chloroplasts and numerous mitochondria. Plastoglobuli are frequently associated with thylakoidal membranes that encircle an internal pyrenoid. The Golgi apparatus has large, club-shaped cisternae. The haptonema consists of 9 microtubules within the cytoplasm, but 6 or 7 microtubules in the external portion. A rootlet system anchors the two flagella that are sub-apically inserted adjacent to the haptonema. The flagellar complex is anchored in the cytoplasm by a flat ribbon of microtubules and microtubular rootlets associated with each basal body. Fibrous rootlets, several of which are cross-banded, interconnect the two flagellar basal bodies and haptonema. ConclusionThree freshwater, scale-less Chrysochromulina isolates are almost indistinguishable in ultrastructure, even though extensive genome sequencing studies verify their distinctiveness. These freshwater representatives certainly comprise members of a cryptic species complex. Extensive morphological similarity also occurs between freshwater and scaled marine isolates. Importantly, this report addresses the misidentification of Chrysochromulina tobinii Cattolico as Chrysochromulina parva Lackey and clarifies a complex literature regarding the morphological description of the type species for this algal clade.