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Millerichthys robustus is the only annual killifish distributed in America with phenotypic color variations, not yet described. Accordingly, we first describe the color pattern in both sexes to define its phenotypical variations. We then analyze the frequency of these phenotypes on a geographical scale, in four localities that represent opposite points of Millerichthys’s distribution in the Mexican southeast. Color analysis based on the RGB system allowed us to define five-color phenotypes in males continuously distributed in various perceptual units between two extreme colors (yellow-red): yellow, moderate orange, dark orange, strong orange and red. These color patterns found in M. robustus could be attributed to melanin, carotenoid, and pteridine pigments. The orange phenotypes was present in all localities studied. The yellow phenotype was present only in northeastern and northwestern locations, and the red phenotype was present only in northern populations. Female color variations were observed in the number of ocelli (from 1 to 15) at the base of the caudal peduncle and dorsal region. Ocelli have been associated with anti-predator functions because they resemble the eyes of vertebrates, thus shifting the target of predator attacks to less vital body parts. Females with 3 ocelli were the most frequent phenotype, and females with 13–15 ocelli occurred only in the northern populations. We concluded that male and female of M. robustus are not randomly distributed along their distribution range, which suggest that color phenotypes may react differently to biotic and abiotic factors that probably determine their distribution and frequency within the studied population.