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Submesoscale eddies (1-10 km diameter) were identified using surface velocity observations obtained from a high-frequency radar system (HFR) operated in Todos Santos Bay (TSB), Baja California, Mexico. Eddies were detected through a special case of the Okubo-Weiss parameter for divergent flows in the form of eigenvalues of the Jacobian matrix. The detection method, applied for a surface velocity grid, shows encouraging results in the recognition and tracking of submesoscale features in TSB. The detection method is rapid and efficient. Results show the formation and persistence of an eddy structure inside the Bay in December 6, 2010, displaying a trajectory from NE to SW until disappearing at the center of the Bay. The eddy is approximately 4 km in diameter with a frequency of ~0.1f (f is the Coriolis parameter). The real part of the Okubo-Weiss parameter ranged between − 4 × 10 − 9 to − 1 × 10 − 9 s − 2, and outlined the eddy for approximately 9 hours. Although it is difficult to identify the origin of the detected submesoscale eddy, its appearance coincided with a drop in relative atmospheric humidity suggesting land-ocean Santa Ana winds as a possible generating mechanism.