Despite considerable morphological differentiation Citrus, Fortunella, Poncirus, Microcitrus and Eremocitrus genera are sexually compatible. Species of these genera are mainly diploid (2n=18). If the origin of cultivated Citrus from four basic taxa (C. maxima, C. medica, C. reticulata and C. micrantha) is now well documented, their phylogenetic relationships with Citrus wild species and related genera is still unclear. In the present work we analyse their nuclear and maternal phylogeny by using respectively SNPs on gene sequences and mitochondrial InDels. A total of 7.15 kb were amplified by PCR from 11 genes (Table1) and sequenced (Sanger) for 33 genotypes. The varietal sample was composed of 7 C. reticulata, 5 C. maxima, 5 C. medica, 4 papeda, 5 Fortunella, 3 Poncirus, 2 Microcitrus, 1 Eremocitrus. Severinia buxifolia was used as outgroup. SNPs were mined using BioEdit and SeqMan softwares and phylogenetic analysis done in http://phylemon.bioinfo.cipf.es with different approaches (Phylip (v. 3.68), Phyml Best AIC Tree (v. 1.02b), PhyML (v. 3.00). For maternal phylogeny, 4 InDel markers developed by (Froelicher et al. 2011) have been used. The average frequency per Kb of SNPs and InDels were respectively 59.88 and 1.33 in coding region and 110.99 and 16.31 in non-coding ones. A total of 506 SNP and 23 InDels were identified (Table1). Within Citrus, the papeda group was the most polymorphic species, with 185 polymorphisms, followed by C. reticulata (125), C. maxima (48), and C. medica (27). A newmitotype was observed for Microcitrus australasica while two different mitotypes were identified for Fortunella. Nuclear and mitochondrial phylogenetic analysis reveal that C. reticulata and Fortunella form a consistent clade clearly differentiated from the clade including the other basic taxa of cultivated citrus (C. maxima, C. medica and C. micrantha).. Inclusion of more genes sequences is undergoing and will improve the resolution of the phylogenetic analysis.