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Spherical cells were detected in low salinity waters during a bloom of Karenia brevis in Alabama coastal waters. These balls resembled K. brevis in size and organelle appearance, contained similar concentration of brevetoxin, and occurred during ongoing K. brevis bloom. Based on the environmental conditions in which these cells were observed, we speculate that a rapid drop in salinity triggered the sphere formation in K. brevis. Brevetoxin concentrations were comparable between surface water samples containing typical and atypical cells ranging from 1 to 10 ng/mL brevetoxin-3 equivalents. Accurate identification and quantification of cell abundance in the water column is essential for routine monitoring of coastal waters, so misidentification of these spherical cells may result in significant underestimation of cell densities, and consequently, brevetoxin level. These potential discrepancies may negatively impact the quality of regulatory decisions and their impact on shellfish harvest area closures. We demonstrate that traditional monitoring based on microscopy alone is not sufficient for brevetoxin detection, and supporting toxin data is necessary to evaluate potential risk.