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The fundamental role of fish is to maintain the balance in the ecosystem, due to their adaptability. Genetic diversity and chromosomal structure reflect evolutionary biology through karyotyping, chromosome banding, and fluorescent hybridization techniques and allow us to understand the biology of fish. Cytogenetic analysis defines morphologically similar species. The variability in the configuration of sex chromosomes in fish shows high evolutionary plasticity and notable diversity, a characteristic of flexibility and variability that allows better environmental adaptation. The presence of B chromosomes, considered genomic parasites, increases the genetic variability of a population by acting as a reservoir of genetic material and induces chromosomal rearrangements, which makes them bioindicators. The micronucleus test, used in aquatic toxicology, to identify chromosomal fragments reflects genetic damage and chromosomal instability. Ancestral karyotypes, a reflection of the complexity of chromosomal evolution, highlight evolutionary implications in fish lineages. The challenge of future cytogenetic research in fish is based on the development of molecular biology technologies or others such as chromosome painting, single-nucleus polymorphism analysis, and sequencing, tools that have served to provide insight into the organization of genomics, its chromosomal evolution and species differentiation. It is concluded that through cytogenetics, the understanding of chromosomal evolution, management in aquaculture, conservation of endangered species, and indicators of aquatic environmental health is facilitated.