Cultivated Citrus result from genome admixtures of four ancestral taxa (C. reticula, C. maxima, C. medica and C. micrantha). Phylogenomics is therefore a key to decipher the origin of modern varieties and to understand the molecular basis of phenotypic variability. Next Generation Sequencing technologies have considerably modified our capacity to explore genomic variation and to understand the complex citrus genomic. However, low cost discrete scan of the genome with highly reliable markers may be sufficient to answer numerous research questions. 454 and Sanger sequencing data of gene fragments dispersed on the nine chromosomes were used to select SNPs totally discriminant of each of the four basic taxa (DSNPs). One hundred fifty selected DSNPs were successfully converted into KASPar markers and provided highly reliable genotyping in diploid and polyploid citrus. They were applied to analyse the origin of secondary citrus species and modern varieties. DSNPs are also very useful (i) to routinely identify zygotic seedlings of citrus rootstocks deriving from direct hybridization between ancestral taxa (ie: Sour orange = C. reticulata x C. maxima, Rough lemon, Volkamer lemon, Rangpur lime: C. reticula x C. medica; Alemow: C. micrantha x C. medica),.(ii) to analyse meiotic mechanisms (2n gametes, tetraploid meiosis) of secondary citrus species and (iii) to trace candidate gene phylogeny in citrus germplasm or recombining progenies. (Texte intégral)