Apteronotus include a large number of recognized species, but few have been cytogenetically studied. This study establishes the first cytogenetic description of A. ellisi collected from the upper Paraguay River basin, which presented 2n=52 chromosomes, karyotype composed of 20 metacentric, 20 submetacentric, eight subtelocentric and four acrocentric chromosomes, and fundamental number as 100 for both sexes. Heteromorphic sex chromosomes were absent. A pair of nucleolar organizing regions (NORs) was detected in the submetacentric chromosome pair 13 by silver-staining. Heterochromatic regions were observed in the long arms of the NOR-bearing chromosome pair. Besides the present data are valuable to help in understanding karyotypic evolution in Apteronotidae. Data from NORs confirmed the tendency of this family in presenting simple NORs sites, similar to the other Gymnotiformes clades. Yet, the presence of little heterochromatin can be used as cytogenetic markers for A. Ellis, and centric fusions/fissions appear to be an important mechanism in the karyotype evolution and differentiation among Apteronotus species.