Fluorescence in situ hybridization (FISH) is a powerful technique for localizing cloned DNA probes directly onto metaphase chromosomes and/or interphase nuclei [1,2]. This technique is a prerequisite tool for genome analysis, and the high topographic resolution of FISH has found widespread applications. Genome mapping in vertebrates using FISH has been significantly enhanced by the development of several new techniques, e.g., high-resolution gene mapping with direct R-banding FISH, multi-color FISH, fiber-FISH, comparative genomic hybridization and chromosome painting with chromosome-specific DNA probes. The development of equipment and computer software for digital imaging has also led to rapid progress in the areas of resolution and efficiency of FISH analysis [3-5]. FISH techniques can be applied to genome research not only in species for which genome information and resources are abundant, but also for map-poor species, for which FISH is quite useful for constructing chromosome maps and for investigating their karyotypic evolution. Furthermore, the molecular cytogenetic data on chromosomal homology allow the transfer of genomic information from maprich species such as humans and mice to a wide variety of other species [6]. We here introduce the application of FISH techniques to comparative genomics of vertebrates, citing examples of our comparative cytogenetic studies of birds and reptiles, which have not been spotlighted for a long period of time in this field.