The majority of species of the Antarctic coastal fish fauna is represented today by the perciform suborder Notothenioidei. The separation of basal lineages of notothenioids has been estimated to have occurred between 23 and 22 million years ago (m.y.a.), while a major diversification probably occurred 16–10 m.y.a. Cytogenetic approaches aim to study the genomic change that, at the cell level, accompanied the radiation of this group. The information available for 66 of 120–130 species makes possible the description of the main patterns of chromosome diversification within the suborder. Within some families (Channichthyidae, Artedidraconidae) the range of the chromosomal variability seems to be minimal whilst the high karyotypic diversity of Nototheniidae and Bathydraconidae is consistent with morphological and molecular data suggesting the paraphyletic nature of these two taxa. Molecular cytogenetics allows detailed chromosome characterization, including mapping of ribosomal genes and of telomeric sequences, thus providing information on processes of karyotypic rearrangement and direction of chromosomal change. Active process of genomic restructuring leads to intraspecific variability in several species, at different levels of chromosomal organization. The growing amount of information make it possible to use notothenioids as a model for testing hypotheses of evolutionary change in marine organisms, including chromosomal diversification.