The effect of two diets (live food and dry diet) and two different populations of Rhamdia quelen from Argentina (pampean and northeastern area) on performance and skeletal deformities in fish larvae, according to a 2x2 factorial design, was evaluated. At the end of the trial (20 days post-hatching), skeletal deformities were diverse and affected all regions of the vertebral axis. In neither case, these anomalies had an impact on final weight of larvae. The northeastern biotype presented the highest percentage of skeletal abnormalities (72.3%) and lower survival. A high incidence of fused and compressed vertebrae (affecting 22.2 and 19.4% of the larvae, respectively) was observed. Statistical analysis showed that fusions were not affected by the biotype or feeding treatment. However, in the case of compressions, interaction between diet and biotype was found. For this kind of malformations, live food treatment shows not difference between biotypes, while larvae fed dry diet had the highest frequency in the northeastern biotype. These results indicate that to prevent the incidence of bone malformations in R. quelen larvae both factors must be considered (biotype and diet). The differential bone and cartilage staining could be a useful tool for precociously detection of skeletal malformations during early developmental stage in R. quelen larvae.