The detection and analysis of DNA polymorphisms in crops is an essential component of marker-assisted selection and cultivar identification in plant breeding. We have explored several molecular techniques which allow to detect a DNA polymorphism: isozymes, amplification of microsatellite interspaced DNA sequences (AMIS), random PCR amplified polymorphic DNA (RAPD) and restriction fragment lenght polymorphism (RFLP). Number of problems in citrus breeding and systematics can be approached using these techniques: (i) molecular markers provide a more direct method to screen a large number of plants, at early development stages; (ii) genetic origin identification (paternity or nucellar/zygotic origin); (iii) genetic linkage map construction to locate genes involved in the development of agronomically interesting characters; markers associated with these genes could then be used for early selection of progenies and possible progenitors for breeding programmes; (iiii) in new breeding schemes employing somatic hybridization these molecular markers are essential to control the genetic composition of the vitroplantelets and calli arising from protoplast fusion. Actually, the microsatellite marker seems to be the most valuable tool in genetic studies and appears very promising in all breeding applications.