Karyotypic analyses have several applications in studies of chromosome organization, evolution, and cytotaxonomy. They are also essential to genome assembly projects. Here, we present for the first time the karyotype description of the endangered species yellow cardinal, Gubernatrix cristata (Passeriformes, Thraupidae), using conventional staining with Giemsa and 18S rDNA probes. This species has 78 chromosomes, with 12 pairs of macrochromosomes and 27 microchromosome pairs. The 18S rDNA clusters were found in four microchromosomes. Our results revealed that G. cristata has a typical avian karyotype (approximately 80 chromosomes). However, G. cristata has an apomorphic state in relation to the 18S rDNA distribution since the ancestral condition corresponds to only two microchromosomes with these sequences. Probably, duplications and translocations were responsible for increasing the number of 18S rDNA clusters in G. cristata. The results were compared and discussed with respect to other Thraupidae and Passeriformes members. Considering the globally threatened status of G. cristata, we believe that its karyotype description could be a starting point for future cytogenetics and sequencing projects.