We present a concept that summarizes the pattern of occurrence of widely distributed organisms with large chromosomal diversity, low molecular divergence, and the absence of morphological identity. Our model is based on cytogenetic and molecular data of four populations of the siluriform Hypostomus ancistroides presented in this study in comparison with those of 15 other previously described populations but is applicable to any group of sister species, chronospecies, or cryptic species. Through the evaluation of karyotype macrostructure and physical location of genes, in addition to phylogenetic reconstructions from mitochondrial and nuclear genes, we observed morphologically indistinguishable individuals presenting different locally fixed karyomorphs with phylogeographic discontinuity. The process behind this pattern seen in many groups of cryptic species, in which variation lies mainly in the organization of their genomes but not necessarily in the ecosystems they inhabit or in their external morphology, is similar to the processes behind other events observed in the distribution of lineages. In this work we explain this pattern through the hypothesis of the existence of a process analogous to ecological-evolutionary radiation, the chromosomal radiation, which can be adaptive or non-adaptive, and explore the possibility of applying the concept of chromosomal radiation to different groups of organisms.