In this special issue, researchers show an updated, complete picture of living reptiles' cytogenetic, genomic, and molecular evolution. The most recent and relevant results of conventional and molecular studies are reported. A possible evolutionary model of the reptiles' chromosome is presented based on chromosome painting and mapping results. Morphology, structure, and molecular composition of reptiles' chromosomes are discussed. Specific topics include the presence and evolution of transposable elements, Hox genes, genome size and composition, and the level heterochromatin methylation. Sex chromosome evolution, mechanisms of meiotic recombination, and the evolution and chromosome localization of specific repetitive DNAs are also examined. This publication is of great interest for all students of cytogenetics, zoology, evolutionary biology, and molecular biology.