The length-weight relationship (LWR) was used to test differences in the fish somatic condition factor among four populations of the endangered desert pupfish, Cyprinodon macularius, from the Lower Colorado River Basin, Mexico. Bimonthly fish sampling and habitat assessments were carried out from September 1996 to August 1997 for four sites in Baja California and Sonora. Slope b of the WLR varied from 3.238 (Cerro Prieto population) to 3.613 (Welton-Mohawk population), showing in all populations a positive allometric growth. Male b values were higher than those of females for Cerro Prieto (3.303 vs 3.071), Welton-Mohawk (3.866 vs 3.579), and Flor del Desierto (3.357 vs 3.169) populations. The Cerro Prieto population showed the highest somatic condition (y-intercept, a = −11.759). Water depth and salinity were the ecological variables that better accounted for most of the variation in the somatic condition of this pupfish, with a negative and a positive effect, respectively.