Cytogenetic studies of genome structure and evolution across taxa often depend on mapping specific tandemly repeated sequences within the genome, using fluorescent probes to determine their location. This protocol offers a simple and flexible approach to mapping medium-to-high copy number tandem repeats in multiple Drosophila tissues. We demonstrate the approach in brains, where we use mitotic chromosomes from larval neuroblasts to identify the chromosomal location of specific repetitive DNA sequences, and in testes, where we type sperm based on repeat composition.