Fluorescencein situhybridization (FISH) was used to localize rDNA sites in relation to heterochromatic regions revealed by double chromomycin A3(CMA) and 4′-6-diamidino-2-phenylindole (DAPI) in somatic chromosomes of Meiwa kumquat (Fortunella crassifoliaSwing.). Four sites were observed, all corresponding to CMA positive regions. Two of them were located in the centromeric region of the two chromosomes with three CMA bands (type A chromosome), and the other two, in the long arm's terminal region of the chromosomes with terminal CMA bands on both telomeres (type C). These sites were of different sizes among probable homologous chromosomes, most likely due to a hybrid origin of this accession. The sites located in the type C chromosomes represent a new locus of rRNA genes in these taxa, suggesting that different evolutionary pathways may lead to a similar heterochromatin distribution, and, hence, that chromosomes with the same CMA banding pattern among different species may not always be homoeologous.