Fluorescence in situ hybridization (FISH) is a powerful technology for studying eukaryotic chromosomes and genomes from the combined view of cytogenetics and molecular biology, but its use in filamentous fungi has been limited. In this chapter, we describe protocols to perform three basic FISH techniques in filamentous fungi: (a) FISH mapping of unique sequences on the somatic chromosomes and interphase nuclei, (b) chromosome painting to detect a specific chromosome in the genome by fluorescent painting of the whole chromosome, and (c) fiber FISH on the stretched DNA fibers for physical mapping. The ways of preparing target specimens unique to filamentous fungi are included in the protocols.