Observations of skeletal malformations in fish in the wild are poorly documented and need to be investigated. Here we report the occurrence of body shortening in specimens of Plagioscion squamosissimus collected in the Volta Grande do Xingu, middle Xingu River region (Pará, Brazil), during a 12-month monitoring program (2021–2022). We observed morphological anomalies in nine individuals, of which two underwent radiographic analysis, recording the fusion and compression of vertebrae in different portions of the spine. The average percentage decrease in body length resulting from the deformity was 23.8%. This is the first record of malformation in this species.