<p>Pygmy angelfishes (Pomacanthidae, <i>Centropyge</i>), with their bright colors and small size, constitute the most diverse clade of the angelfishes (Pomacanthidae). Their phylogenetic relationships indicate a main biogeographical distribution in the Indo-Pacific or Central Pacific with recent dispersal to the Atlantic Ocean. Unlike the more conservative pattern of chromosomal evolution of other angelfishes, <i>Centropyge</i> has a more dynamic pattern of karyotypic diversification, whose intrinsic association with the organization of repetitive sequences and its relation to the phylogenetic and biogeographical aspects yet are unknown. Here, are presented cytogenetic data and mapping of different classes of repetitive DNA (rDNA, microsatellites and <i>Rex3</i> elements) in the chromosomes of <i>C. aurantonotus</i>, Flameback angelfish and <i>C. eibli</i>, Blacktail angelfish and its association with biogeographic and phylogenetic patterns of this group. The species <i>C. eibli</i> (2n = 48; 48a) and <i>C. aurantonotus</i> (2n = 48; 4&#xa0;m + 14sm + 26st + 4a) differ significantly in their karyotypic pattern. In these species, the (CA)₁₅ and (CGG)₁₀ repeats and <i>Rex3</i> elements are distributed mainly in centromeric and pericentromeric regions of the chromosomes. 18S rDNA sequences occur in one locus on a large acrocentric chromosome in the species, while 5S rDNA sites occupy one locus in <i>C. eibli</i>, and nine loci in <i>C. aurantonotus</i>. The growing karyotypic diversification presented by <i>Centropyge</i> groups subjected to expansion to new areas, suggest the contrasting karyotype divergence in pygmy angelfish as a byproduct of evolutionary processes derived of vicariance events, dispersion pattern, and adaptative pressures during evolutionary divergence among their clades.</p>