The Pou2 and Sox2 proteins are major transcription factors for development and cell differentiation. In teleosts, the expression patterns of pou2 or sox2 are different between species from distant families, suggesting different regulatory mechanisms of gene expression. In this study, we assessed the divergences among teleosts, including within closely related species. The pou2 and sox2 gene expression patterns were characterised over several developmental stages in a cyprinid model, i.e., the goldfish, and the potential regulation sites of these genes within teleost conserved regions were localised. During embryonic development, differences in the expression patterns between the goldfish and other teleosts, including zebrafish, were observed for both genes. The in silico analysis of the 5' flanking regions of the pou2 gene showed high conservation within teleosts, whereas the sox2 sequence diverged in tetraodontiforms. Certain putative cis regulatory elements were common to all teleosts, whereas others were found only in cyprinids. The analysis of the DNA methylation patterns of the pou2 and sox2 upstream sequences revealed that the studied CpG sites remained hypomethylated at all stages of embryo development in both genes. In contrast, in the adult fin, the studied CpG sites were hypermethylated in pou2 but not in sox2, suggesting the existence of methylation-sensitive regions in pou2. Overall, although most similarities at the level of the gene regulatory sites were found within cyprinids, the expression pattern of pou2 or sox2 during development differs between cyprinids species.