In Citrus, the interspecific sexual compatibility, the easy hybridization and the existence of apomixis in many cultivars are factors that explain the large genetic diversity of the genera associated to a wide phenotypic diversity. However, the phylogenetic relationships are controversy for some groups as mandarins and pummelos. Strong phenotypic differences exist on coloration and acidity within these groups and represent important criteria for breeders as well as for fruit and juice market. In this context, the aim of this work was to identify SNPs by in silico analysis from 16, 3 and 19 genes of carotenoids, chlorophyll and sugar metabolic pathways, respectively, based on a comparison of 3 mandarins, 2 pummelos and 5 other Citrus varieties. From the 3,610 SNP markers previously identified, a GST analysis was performed and allowed the selection of 1,386 SNPs separating mandarin and pummelos genotypes. The SNP position (exon/intron) and the distance between two SNPs were parameters for selection of 145 SNPs, which were used in diversity analysis with KASPar chemistry on a larger population of 22 mandarins, 10 pummelos and 64 varieties of lemons, limes, grapefruits and clementines. We confirmed the efficiency of 83 SNPs in separating the mandarin and pummelos interspecific groups. Moreover, 33 SNPs separated genotypes within groups (intraspecificity). This study grave new information on genetic proximity of lemon, grapefruit and clementine varieties with mandarins and pummelos groups. (Texte intégral)