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The genus Atherinella contains 35 species of which the state of Chiapas, Mexico presents 3: Atherinella alvarezi, Atherinella guatemalensis and Atherinella schultzi, which present confusions or records of undescribed forms. The present study was carried out with the purpose of evaluating and comparing morphologically the freshwater species of the genus Atherinella in the state of Chiapas. A total of 101 specimens were evaluated by geometric morphometry and traditional morphometry. The presence of three groups was confirmed and the analyzed specimens do not correspond to the reported species. These results allow us to propose the existence of undescribed taxa that present a morphological variation possibly generated by evolutionary processes such as adaptation and diversification. New taxonomic knowledge of the genus Atherinella in Chiapas, Mexico is provided.