The non-mendelian mode of inheritance of cytoplasmic organelle genomes (mitochondrial and chloroplast) makes the information present in the plant mitochondrial DNA (mtDNA) and chloroplast DNA cpDNA) of great interest for phylogeny. Furthermore, in our protoplast fusion program, we need cytoplasmic molecular markers to study the genetic origin of plantlets obtained from different citrus somatic hybrids in inter-specific and inter-generic combinations, The cpDNA is know to be highly conserved in structure and the substitution rate of plant mitochondrial DNA genes is low and these conserved coding sequences are easily identified. Here we describe the use for Citrus of mitochondrial and chloroplast universal primers corresponding to conserved coding sequences previously selected for population genetic studies in oak (Quercus robur). These primers allow the amplification of interstitial non-coding regions. Variation in cytoplasmic organelles can be detected by coupling amplification and RFLP techniques : The amplified DNA fragments are digested by frequently cutting restriction enzymes and analysed by acrylamide gel electrophoresis.