In addition to microscopically visible chromosomal rearrangements, numerous cryptic chromosome changes have been described since the introduction of techniques such as FISH, array CGH, and MLPA. This is particularly true for dynamic regions in the subtelomeric and subcentromeric regions of all chromosomes. To investigate these regions, locus-specific FISH probes are used as single, chromosome-specific, or genome-wide probe sets. Here, we present the chromosome-specific subtelomere-subcentromere multicolor FISH (subCTM), and genome-wide subcentromere multicolor FISH (subcenM) probe sets, which can be used as screening tools in specific patient groups, such as those with infertility and intellectual disabilities, but also in tumor cytogenetics and for evolutionary studies in the form of ZOO-FISH.