FISH has been extensively studied as a diagnostic technique for the identification of pathogens in the field of medical microbiology. Although it has been proven to be a useful and applicable technique, it is still not widely applied in diagnostic laboratories. The short time to diagnosis (less than 2 hours) has been a major advantage compared with biochemical differentiation, but this advantage is challenged by MALDI-TOF-MS which allows the identification of a wider range of pathogens compared with biochemical differentiation techniques. Using FISH for diagnostic purposes has found its purpose when immediate species identification is needed, specifically for the investigation of blood cultures for which FISH is a cheap and easy technique for preliminary rapid diagnosis.
FISH can also be used to compare the genomes of two biological species, to deduce evolutionary relationships.  A similar hybridization technique is called a zoo blot. Bacterial FISH probes are often primers for the 16s rRNA region.
FISH is widely used in the field of microbial ecology, to identify microorganisms. Biofilms, for example, are composed of complex (often) multi-species bacterial organizations. Preparing DNA probes for one species and performing FISH with this probe allows one to visualize the distribution of this specific species within the biofilm. Preparing probes (in two different colors) for two species allows researchers to visualize/study co-localization of these two species in the biofilm and can be useful in determining the fine architecture of the biofilm.