For the investigation of genes encoding flagellar proteins, the most common use for molecular mapping information is to correlate cloned DNA sequences with known mutant loci. The cloned genomic DNA or cDNA is obtained using insertional mutagenesis or a biochemical approach. Mapping the cloned DNA allows determining whether it is linked to previously mapped mutations affecting flagellar function. Chlamydomonas reinhardtii is a valuable system for molecular genetic studies of flagellar assembly and motility and of basal body function. Mutations in more than 80 genes affecting the function of these organelles have been mapped. A growing number of genes encoding flagellar proteins have been isolated using a variety of methods including differential screening of cDNA libraries and screening of expression libraries with antibodies. Insertional mutagenesis methods developed recently rely on transposable elements or plasmid DNA integrated into the genome by transformation to generate a molecular tag associated with the mutagenized gene that facilitates its isolation. A molecular map anchored on the genetic map is currently available for the Chlamydomonas nuclear genome. The molecular map allows to rapidly establish the genetic map position of cloned genes and to correlate the map positions of these clones with previously mapped mutations. In addition, the molecular map may be useful for positional cloning of genes by genomic walking from a molecular marker to a nearby gene of interest. It may also facilitate the future construction of a physical map of the Chlamydomonas genome based on large cloned overlapping DNA fragments. The existing molecular map has been established primarily with restriction fragment length polymorphism (RFLP) mapping technology and contains genetic and molecular markers.