<p>DNA methylation in eukaryotes happens exclusively in cytosine residues and presents different patterns among species. Methylated portions usually coincide with repetitive regions, like those rich in heterochromatin, and are believed to be related to adjacent genes silencing. The aim of this study was to identify the methylation patterns in two populations of armored fish from the complex of cryptic species <i>Hypostomus ancistroides</i> from the Alto Paraná river basin (Brazil) in which a sexual chromosome system is present in one (<i>H</i>. aff <i>ancistroides</i>) but absent in the other (<i>H. ancistroides</i>). The detection of methylated regions was conducted using immunostaining with the monoclonal antibody anti-5-methylcytosine. Individuals of <i>H. ancistroides</i> presented a corresponding pattern between methylation and heterochromatin regions. Individuals of <i>H.</i> aff. <i>ancistroides</i>, on the other hand, presented positive markings in almost all chromosome of complements. There were also differences between the sex: males present a hypermethylated chromosome complement, and females had a few markings in the chromosomes or only centromeric or subterminal regions methylated. X and Y sex chromosomes were identified as almost fully methylated. A possible explanation for such differences may be the association of heterochromatin formation processes and the presence of transposable elements. However, despite the existence of studies that identify the location of methylation regions in genomes, their influence and interaction with karyotypes are not yet well known in fish. In any case, individual variations in methylation patterns may reflect differences in the role they play in the adaptive process, gene expression and evolutionary history of each group.</p>