Poncirus trifoliata (L.) Rat. and its hybrids are part of the citrus germplasm very useful for rootstock breeding. Taking into account the difficulties to isolate good quality protoplasts from leaves of field trees, the failure of nucellar embryogenic callus induction from these genotypes and the risk of zygotic plant recovery among the seedlings, il is important Io establish genetically certified in vitro fines for further protoplast isolation with the objective of developing new strategies involving somatic hybridization. Micropropagation allows the obtention of genetically homogeneous plantlets and il is a way to attain such kind of fines. However, it is important to control the genetic homogeneity of the micropropagated plants. Isozyme, sequence-tagged microsatellite sites (STMS), and flow cytometry analysis developed in various citrus species allow to control sonne major sources of variation such as zygotic origin of the explants or ploidy variafion. The résults of the usefulness of these techniques in the control of the genetic homogeneity of micropropagated shoots of Troyer citrange [Citrus sinensis (L.) Osb. x Poncirus trifoliala (L.) Rat.], Rubidoux trifoliate orange [Poncirus trifoliata (L.) Raf.], and Poncirus trifoliata var. Flying dragon are presented. The selected fines will be used in research works to continue the creation of new rootstocks through somatic hybridization.