Cryptobia iubilans, the reported etiologic agent of gastric cryptobiosis, is a common flagellate parasite infecting the gastrointestinal tract in ornamental cichlids. The disease results in significant mortality and survivors become carriers that may later recrudesce with disease following stressor events. A presumptive diagnosis is made by identifying the flagellates and/or granulomas in wet mount preparations of the stomach with confirmation provided by histopathology. Lesions vary with chronicity, but are typified by granulomatous inflammation and granuloma formation within the gastric and intestinal wall, with characteristic organisms variably present freely and within macrophage cytoplasm. Parasitic invasion of the gastric wall can result in mural compromise, rupture and coelomitis often accompanied by systemic dissemination and death. The molecular characterization of C. iubilans and diversity of flagellates associated with gastric cryptobiosis of cichlids is unknown as Cryptobia speciation has relied predominantly on ultrastructural morphometrics. Clinical and pathologic findings associated with a gastric cryptobiosis outbreak, ultrastructural and molecular characterization of the parasite, and retrospective molecular characterization of parasite diversity associated with archived cases in African and South American cichlids will be discussed.