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The population morphometric variation of the endangered freshwater killifish (Fundulus lima) was evaluated and compared with that of its euryhaline coastal relatives (F. parvipinnis parvipinnis and F. p. brevis) on the basis of 384 specimens from the Baja California peninsula, Mexico. Forty five standardized body distances were compared by means of discriminant function analysis (DFA). Sixteen body distances were significant to distinguish two groups of populations for F. lima: a first group represented by the Bebelamas and San Javier basins, and second group composed by the basins of San Ignacio, La Purisima, San Luis, San Pedro and Las Pocitas. When all freshwater and coastal populations were compared, the southernmost population of F. lima (Las Pocitas) showed a higher morphometric similarity with the southern coastal subspecies (F. p. brevis), while another southern population (San Pedro) had an intermediate position between the freshwater and coastal forms. This study suggests the presence of five evolutionary units (three freshwater and two coastal) for the genus Fundulus in the Baja California peninsula.