A quantification of intraspecific variation in morphological traits is necessary not only as a basis for taxonomic work but also to understand a basic aspect of evolution. Comparisons among species could reveal differences in plasticity in development among them and even give clues on evolvability. Studies of this kind are rare for extinct species of vertebrates given the lack of adequate samples, but there are notable exceptions. Morphometric and meristic data were collected for three species of fossil killifish in order to quantify intraspecific variation: 67 specimens of Prolebias rhenanus from the Lower Oligocene of Baden-Württemberg, 40 specimens of Pr. stenoura from the Lower Oligocene of Puy-de-Dôme, and 141 specimens of Paralebias cephalotes from the Upper Oligocene of Aix-en-Provence. Nearly identical patterns of intraspecific variation exist between the two species of Prolebias. Fin base lengths and precaudal lengths of the vertebral column are the most variable traits in both species, followed by pterygiophore counts, then other axial length measurements and, least variable, vertebral counts. In neither species was there a significant difference in observed variation between fin and vertebral or meristic and morphometric traits. The only significant correlation shared between the two species is the positive relationship between caudal length of the vertebral column and length of the anal fin base. Precaudal length of the vertebral column is less variable in Paralebias than in Prolebias, while precaudal vertebral count is more variable, in absolute values of the coefficient of variation. Variability in elongation of precaudal vertebrae may be the underlying cause of the absence of correlation between decreased variation in precaudal length of the vertebral column and increased variation in precaudal count in Paralebias cephalotes. We report more similar patterns of variation among Prolebias congeners than between Prolebias and Paralebias, suggesting that trait variability is changing over evolutionary time in this actinopterygian lineage.