Somatic hybridization by protoplast fusion is a very useful technique for citrus rootstock breeding. Indeed, it theoretically allows the accumulation of all genes of the parents, irrespective of their heterozygosity level and therefore the addition of complementary dominant traits. In this work, protoplasts were isolated from callus of Citrus macrophylla and from leaves of 'Carrizo' citrange (C. sinensis × P. trifoliata). Chemical, electro-chemical and electric fusions were performed and the ploidy of regenerated plants was evaluated by flow-cytometry. Five tetraploid plants, one pentaploid plant, one mixoploid (3x-6x) plant and one heptaploid plant were recovered. All these plants were analyzed with SSR and SNP markers, distributed in the nine chromosomes of citrus. Cytoplasmic genomes were characterized with chloroplastic and mitochondrial markers. Mitochondrial genome was inherited from C. macrophylla for all plants while segregation was observed for the chloroplastic genome. Nuclear genome analysis revealed the loss of parental alleles in most of the regenerated plants. In tetraploids, it affected mainly C. macrophylla alleles while P. trifoliata alleles were mostly lost in 5x and 7x plants. The results indicate chromosome instability in this complex intergeneric combination with apparent non random loss of some chromosome fragments. Two allotetraploid somatic hybrids have been selected for evaluation as potential rootstocks.