Fluorescence in situ hybridization (FISH) is commonly performed to visualize RNA and DNA. It is routinely used in cytogenetics and karyotyping to check for chromosomal abnormalities and diagnose and identify diseases (Levsky and Singer, J Cell Sci 116:2833-2838, 2003). Oligopaints is a recently established DNA FISH method that has quickly become popular because of its flexibility and economical durability. Oligopaints uses computationally designed PCR-renewable oligonucleotides for probes, which can cover a few kilobases to whole chromosomes (Beliveau, Proc Natl Acad Sci 109:21301-21306, 2012). In addition, different fluorophores can be used for desired probe sets for multicolor imaging. Here, we describe an optimized method for implementing the Oligopaints procedure to visualize genomic regions in Drosophila testis. We further discuss the possibility of resolving local microstructure of specific gene loci.