Somatic hybridization is a powerful biotechnology technique which helps to create new somatic genotypes combining desirable traits from both parents. Nowadays, its use has become an integral part of plant breeding programs. In this study, plants derived from five protoplast fusion combinations, i.e. “Citrus macrophylla + Valencia orange (C. sinensis)”, “C. macrophylla + Kinnow mandarin (C. nobilis × C. deliciosa)”, “Carrizo citrange (C. sinensis × P. trifoliata) + Willow leaf mandarin (C. deliciosa)”, “Volkamer lemon (C. volkameriana) + Willow leaf mandarin” and “Nasnaran mandarin (C. amblycarpa) + Willow leaf mandarin” were subjected to molecular analysis of nuclear and cytoplasmic genome. The use of SSR markers confirmed the formation of hybrids and somatic cybrids within this population. Flow cytometry analysis has further shown that 12 of the 14 regenerated plants were diploid, while two, which originated from the C. macrophylla + Valencia orange combination, were tetraploid. The analysis of cytoplasmic genome using universal primers revealed that chloroplast DNA (cpDNA) of these genotypes was inherited randomly, while their mitochondrial genomes were inherited from the embryonic parents.