Three diploid citrus somatic hybrids (cybrids) were produced by fusions combining nucellar callus-derived protoplasts of Willow Leaf mandarin (Citrus deliciosa Ten.) and Commune clementine (Citrus clementina Hort. ex Tan.) with, respectively, leaf protoplasts of Eureka lemon [Citrus limon (L.) Burm.] and Marumi kumquat [Fortunella japonica (Thunb.) Swing.] and leaf protoplasts of Marumi kumquat. Ploidy and origins of the nuclear, chloroplastic, and mitochondrial genomes were investigated by flow cytometry and nuclear and cytoplasmic simple sequence repeat analyses. Volatile compounds were extracted from the leaves of the three cybrids by a pentane/ether (1:1) mixture, analyzed by GC-MS, and compared to those of their parents. The cybrids were found to be very close to their nucleus-giving parent, suggesting that the main information for volatile compounds biosynthesis is contained in the nucleus. However, nucleo-cytoplasmic interactions occurred: the (mandarin + lemon) cybrid, possessing nucleus and chloroplasts of lemon and mitochondria from mandarin, synthesizes more monoterpene alcohols and esters than its nucleus-giving parent; the (clementine + kumquat) cybrid, possessing nucleus from kumquat and organelles from mandarin, synthesizes more monoterpene and sesquiterpene hydrocarbons and sesquiterpene alcohols than its nucleus-giving parent.