Ctenoluciidae (Characiformes), a family of freshwater fishes, comprises 2 genera, <i>Ctenolucius</i> and <i>Boulengerella</i>, with 7 recognized species. Up to now, only species of the genus <i>Boulengerella</i> have been subjected to cytogenetic studies. Here, we investigated the karyotype and other cytogenetic features of pike characin, <i>Ctenolucius hujeta</i>, using conventional (Giemsa staining, C-banding, Ag-NOR staining) and molecular (rDNA, telomeric sequences, and fiber-FISH mapping) procedures. This species has a diploid chromosome number of 2n = 36, and a karyotype composed of 12m + 20sm + 4a and FN = 68, similar to that found in <i>Boulengerella</i> species. However, differences regarding the number and distribution of several chromosomal markers support a distinct generic status. Colocalization of the 18S and 5S rDNA genes is an exclusive characteristic of the <i>C. hujeta</i> genome, with an interspersed distribution in the chromosomal fiber, an unusual phenomenon among eukaryotes. Additionally, our results support the view that Ctenoluciidae and Lebiasinidae families are closely related.