Often, in biological studies, it is necessary to identify an organism's chromosomes. In some organisms the individual chromosomes can be identified by staining procedures while many other species have a very large number of chromosomes, often of similar size, which defy identification by traditional staining methods. We have devised strategies, based on fluorescent in situ hybridization (FISH), which allow the assignment of a preset number of probes to each chromosome without prior chromosome identification. By hybridizing mixtures of probes labeled with different colored fluorescent molecules, the chromosomal origin of each probe can be determined.